PDB Short entry for 2H5D HEADER HYDROLASE/HYDROLASE INHIBITOR 25-MAY-06 2H5D TITLE 0.9A RESOLUTION CRYSTAL STRUCTURE OF ALPHA-LYTIC PROTEASE COMPLEXED TITLE 2 WITH A TRANSITION STATE ANALOGUE, MEOSUC-ALA-ALA-PRO-VAL BORONIC ACID COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALPHA-LYTIC PROTEASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: MATURE PROTEASE DOMAIN (RESIDUES 200-397); COMPND 5 SYNONYM: ALPHA-LYTIC ENDOPEPTIDASE; COMPND 6 EC: 3.4.21.12; COMPND 7 OTHER_DETAILS: GLYCEROL BOUND TO THE CATALYTIC ADDUCT, CREATING A COMPND 8 MIMIC OF THE ACYLATION TRANSITION STATE INTERMEDIATE; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: MEOSUC-ALA-ALA-PRO-ALA BORONIC ACID INHIBITOR; COMPND 11 CHAIN: B; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LYSOBACTER ENZYMOGENES; SOURCE 3 ORGANISM_TAXID: 69; SOURCE 4 SECRETION: SECRETED BY THE NATIVE BACTERIUM; SOURCE 5 OTHER_DETAILS: GENE ALPHA-LP; SOURCE 6 MOL_ID: 2; SOURCE 7 SYNTHETIC: YES KEYWDS A-LYTIC PROTEASE, SERINE PROTEASE, ACYLATION TRANSITION STATE, KEYWDS 2 CATALYSIS, PROTEIN FOLDING, PROTEIN STABILITY, PACKING DISTORTION, KEYWDS 3 HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR C.N.FUHRMANN,D.A.AGARD REVDAT 6 15-NOV-23 2H5D 1 ATOM REVDAT 5 30-AUG-23 2H5D 1 REMARK LINK REVDAT 4 13-JUL-11 2H5D 1 VERSN REVDAT 3 24-FEB-09 2H5D 1 VERSN REVDAT 2 03-OCT-06 2H5D 1 REMARK REVDAT 1 26-SEP-06 2H5D 0 JRNL AUTH C.N.FUHRMANN,M.D.DAUGHERTY,D.A.AGARD JRNL TITL SUBANGSTROM CRYSTALLOGRAPHY REVEALS THAT SHORT IONIC JRNL TITL 2 HYDROGEN BONDS, AND NOT A HIS-ASP LOW-BARRIER HYDROGEN BOND, JRNL TITL 3 STABILIZE THE TRANSITION STATE IN SERINE PROTEASE CATALYSIS JRNL REF J.AM.CHEM.SOC. V. 128 9086 2006 JRNL REFN ISSN 0002-7863 JRNL PMID 16834383 JRNL DOI 10.1021/JA057721O REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH C.N.FUHRMANN,B.A.KELCH,N.OTA,D.A.AGARD REMARK 1 TITL THE 0.83A RESOLUTION CRYSTAL STRUCTURE OF ALPHA-LYTIC REMARK 1 TITL 2 PROTEASE REVEALS THE DETAILED STRUCTURE OF THE ACTIVE SITE REMARK 1 TITL 3 AND IDENTIFIES A SOURCE OF CONFORMATIONAL STRAIN REMARK 1 REF J.MOL.BIOL. V. 338 999 2004 REMARK 1 REFN ISSN 0022-2836 REMARK 1 REFERENCE 2 REMARK 1 AUTH R.BONE,D.FRANK,C.A.KETTNER,D.A.AGARD REMARK 1 TITL STRUCTURAL ANALYSIS OF SPECIFICITY: ALPHA-LYTIC PROTEASE REMARK 1 TITL 2 COMPLEXES WITH ANALOGUES OF REACTION INTERMEDIATES REMARK 1 REF BIOCHEMISTRY V. 28 7600 1989 REMARK 1 REFN ISSN 0006-2960 REMARK 2 REMARK 2 RESOLUTION. 0.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 0.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 CROSS-VALIDATION METHOD : FREE R REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.081 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.080 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.091 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.003 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 7352 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 146962 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.072 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.082 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 6543 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 130332 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1424 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 45 REMARK 3 SOLVENT ATOMS : 432 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 1784.3 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 1367.2 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 21 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 20128 REMARK 3 NUMBER OF RESTRAINTS : 23688 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.016 REMARK 3 ANGLE DISTANCES (A) : 0.045 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.035 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.081 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.070 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.000 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.005 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.038 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.086 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH & HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGEN ATOMS WERE INCLUDED IN THE REMARK 3 REFINEMENT AS "RIDING HYDROGENS", WITH POSITION AND GEOMETRY REMARK 3 FIXED TO THOSE VALUES DEFINED BY SHELXL-97. METHYL AND HYDROXYL REMARK 3 HYDROGENS ON SINGLE-CONFORMER SIDECHAINS WERE EACH POSITIONED AT REMARK 3 A TORSION ANGLE THAT BEST SATISFIED POSITIVE DIFFERENCE ELECTRON REMARK 3 DENSITY (USING INSTRUCTIONS HFIX 137 AND HFIX 147, RESPECTIVELY) REMARK 3 . IT SHOULD BE NOTED THAT THE LENGTH OF DONOR-HYDROGEN BONDS IN REMARK 3 THIS STRUCTURE ARE LIKELY SHORTER THAN THEIR TRUE INTERNUCLEAR REMARK 3 DISTANCE; THESE BOND LENGTHS ARE DEFINED BY SHELXL-97 REMARK 3 PARAMETERS. THE POSITIONS OF SEVEN HYDROGEN ATOMS WERE ALLOWED REMARK 3 TO REFINE FREELY: HIS57 HD1, HIS57 HE1, HIS57 HE2, SER214 HG, REMARK 3 SER195 HN, GLY193 HN, AND B2V203 H1. DURING THE FINAL STAGES OF REMARK 3 REFINEMENT, GEOMETRICAL RESTRAINTS WERE RELEASED FOR ALL NON- REMARK 3 HYDROGEN ATOMS IN RESIDUES WITH SINGLE CONFORMATIONS. THE BORON REMARK 3 IN RESIDUE B2V WAS REFINED AS A CARBON ATOM, ALLOWING REFINEMENT REMARK 3 OF THE OCCUPANCY OF THIS ATOM TO ESTIMATE THE ELECTRON CONTENT REMARK 3 (AND NEGATIVE CHARGE) AT THIS LOCATION. TO AID THE READER IN REMARK 3 ANALYZING THE STRUCTURE IN THIS PDB FILE, THE ATOM HAS BEEN RE- REMARK 3 NAMED TO "B", AND THE OCCUPANCY OF THE BORON ATOM MANUALLY REMARK 3 CHANGED TO THE CORRESPONDING OCCUPANCY (1.07; REFINEMENT OF A REMARK 3 CARBON IN THIS POSITION RESULTED IN AN OCCUPANCY OF 0.89). SEE REMARK 3 PUBLICATION FOR MORE DETAILS. REMARK 4 REMARK 4 2H5D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-MAY-06. REMARK 100 THE DEPOSITION ID IS D_1000037949. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-JUN-04 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 8.00 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.2.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.75 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL, SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 147100 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.900 REMARK 200 RESOLUTION RANGE LOW (A) : 28.500 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 8.700 REMARK 200 R MERGE (I) : 0.08500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 27.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.91 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : 5.90 REMARK 200 R MERGE FOR SHELL (I) : 0.44800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: REFINEMENT OF PREVIOUSLY REMARK 200 -SOLVED STRUCTURE OF ALPHA-LYTIC PROTEASE BOUND TO MEOSUC-ALA- REMARK 200 ALA-PRO-ALA BORONIC ACID REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: SAME PROTEIN BOUND TO MEOSUC-ALA-ALA-PRO-ALA REMARK 200 BORONIC ACID AT 0.9A RESOLUTION (UNPUBLISHED DATA, BUT RELATED REMARK 200 TO 1P02) REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.44 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.3M LITHIUM SULFATE, 0.02M TRIS, PH REMARK 280 8.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K, PH 8.00 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 53.03600 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 26.51800 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 26.51800 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 53.03600 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2280 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8060 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -81.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 595 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 604 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 605 LIES ON A SPECIAL POSITION. REMARK 400 REMARK 400 COMPOUND REMARK 400 REMARK 400 THE METHOXYSUCCINYL-ALA-ALA-PRO-VALINE BORONIC ACID IS PEPTIDE-LIKE, REMARK 400 A MEMBER OF INHIBITOR CLASS. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: METHOXYSUCCINYL-ALA-ALA-PRO-VALINE BORONIC ACID REMARK 400 CHAIN: B REMARK 400 COMPONENT_1: PEPTIDE LIKE POLYMER REMARK 400 DESCRIPTION: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O3 SO4 A 252 O HOH A 533 0.84 REMARK 500 S SO4 A 252 O HOH A 533 0.98 REMARK 500 HH11 ARG A 141 HG1 THR A 142 1.28 REMARK 500 O2 B2V B 203 C2 GOL B 204 1.39 REMARK 500 O2 B2V B 203 C2 GOL B 204 1.39 REMARK 500 O2 B2V B 203 C2 GOL B 204 1.44 REMARK 500 O2 SO4 A 252 O HOH A 533 1.69 REMARK 500 O1 SO4 A 252 O HOH A 533 1.98 REMARK 500 O HOH A 424 O HOH A 631 2.11 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 ARG A 178 CZ ARG A 178 NH2 0.079 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 48A CD - NE - CZ ANGL. DEV. = 10.6 DEGREES REMARK 500 ARG A 48A NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 ARG A 48A NE - CZ - NH2 ANGL. DEV. = -4.1 DEGREES REMARK 500 ARG A 90 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 ARG A 120A NE - CZ - NH1 ANGL. DEV. = -4.6 DEGREES REMARK 500 ARG A 120A NE - CZ - NH2 ANGL. DEV. = 4.1 DEGREES REMARK 500 ARG A 141 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG A 178 NE - CZ - NH1 ANGL. DEV. = -4.5 DEGREES REMARK 500 SER A 201A O - C - N ANGL. DEV. = -12.1 DEGREES REMARK 500 ARG A 230 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 ARG A 230 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 LEU A 242 O - C - N ANGL. DEV. = 9.7 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ALA A 39 -91.46 -132.71 REMARK 500 ARG A 48A 87.62 -153.32 REMARK 500 ASN A 60 -1.55 80.89 REMARK 500 PRO A 95 -155.33 -77.48 REMARK 500 PRO A 120 49.66 -87.23 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 138 0.10 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 LEU A 41 -14.82 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 GLYCEROL BOUND TO THE CATALYTIC ADDUCT, CREATING A MIMIC OF THE REMARK 600 ACYLATION TRANSITION STATE INTERMEDIATE REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 GOL B 204 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 246 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 208 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 247 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 248 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 249 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 250 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 251 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 252 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN B OF MEOSUC-ALA-ALA-PRO REMARK 800 -ALA BORONIC ACID INHIBITOR REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1SSX RELATED DB: PDB REMARK 900 SAME PROTEIN AT PH 8 (0.83A RESOLUTION) REMARK 900 RELATED ID: 1TAL RELATED DB: PDB REMARK 900 SAME PROTEIN AT PH 8 (1.5A RESOLUTION) REMARK 900 RELATED ID: 2ULL RELATED DB: PDB REMARK 900 DATA FROM 1TAL WERE MODELED HERE WITH 16 CONFORMATIONS OF THE REMARK 900 ENTIRE PROTEIN REMARK 900 RELATED ID: 1QRX RELATED DB: PDB REMARK 900 SAME PROTEIN AT PH 5.14 (1.6A RESOLUTION) REMARK 900 RELATED ID: 2H5C RELATED DB: PDB REMARK 900 APO ENZYME AT PH 5 (0.82A RESOLUTION), ANOTHER MIMIC OF THE REMARK 900 TRANSITION STATES REMARK 900 RELATED ID: 1P03 RELATED DB: PDB REMARK 900 2.15A RESOLUTION STRUCTURE OF SAME PROTEIN BOUND TO SAME INHIBITOR, REMARK 900 WITHOUT GLYCEROL IN THE BINDING POCKET DBREF 2H5D A 15A 245 UNP P00778 PRLA_LYSEN 200 397 DBREF 2H5D B 199 203 PDB 2H5D 2H5D 199 203 SEQRES 1 A 198 ALA ASN ILE VAL GLY GLY ILE GLU TYR SER ILE ASN ASN SEQRES 2 A 198 ALA SER LEU CYS SER VAL GLY PHE SER VAL THR ARG GLY SEQRES 3 A 198 ALA THR LYS GLY PHE VAL THR ALA GLY HIS CYS GLY THR SEQRES 4 A 198 VAL ASN ALA THR ALA ARG ILE GLY GLY ALA VAL VAL GLY SEQRES 5 A 198 THR PHE ALA ALA ARG VAL PHE PRO GLY ASN ASP ARG ALA SEQRES 6 A 198 TRP VAL SER LEU THR SER ALA GLN THR LEU LEU PRO ARG SEQRES 7 A 198 VAL ALA ASN GLY SER SER PHE VAL THR VAL ARG GLY SER SEQRES 8 A 198 THR GLU ALA ALA VAL GLY ALA ALA VAL CYS ARG SER GLY SEQRES 9 A 198 ARG THR THR GLY TYR GLN CYS GLY THR ILE THR ALA LYS SEQRES 10 A 198 ASN VAL THR ALA ASN TYR ALA GLU GLY ALA VAL ARG GLY SEQRES 11 A 198 LEU THR GLN GLY ASN ALA CYS MET GLY ARG GLY ASP SER SEQRES 12 A 198 GLY GLY SER TRP ILE THR SER ALA GLY GLN ALA GLN GLY SEQRES 13 A 198 VAL MET SER GLY GLY ASN VAL GLN SER ASN GLY ASN ASN SEQRES 14 A 198 CYS GLY ILE PRO ALA SER GLN ARG SER SER LEU PHE GLU SEQRES 15 A 198 ARG LEU GLN PRO ILE LEU SER GLN TYR GLY LEU SER LEU SEQRES 16 A 198 VAL THR GLY SEQRES 1 B 5 MSU ALA ALA PRO B2V MODRES 2H5D B2V B 203 VAL VALINE BORONIC ACID HET MSU B 199 16 HET B2V B 203 18 HET SO4 A 246 5 HET SO4 A 247 5 HET SO4 A 248 5 HET SO4 A 249 5 HET SO4 A 250 5 HET SO4 A 251 5 HET SO4 A 252 5 HET SO4 B 208 5 HET GOL B 204 30 HETNAM MSU SUCCINIC ACID MONOMETHYL ESTER HETNAM B2V VALINE BORONIC ACID HETNAM SO4 SULFATE ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 MSU C5 H8 O4 FORMUL 2 B2V C4 H12 B N O2 FORMUL 3 SO4 8(O4 S 2-) FORMUL 11 GOL C3 H8 O3 FORMUL 12 HOH *432(H2 O) HELIX 1 1 ALA A 55 GLY A 59 5 5 HELIX 2 2 PRO A 222A ARG A 224 5 5 HELIX 3 3 LEU A 231 GLY A 239 1 9 SHEET 1 A 3 ASN A 15B GLY A 18 0 SHEET 2 A 3 THR A 113 ASN A 120D 1 O ALA A 120C N GLY A 18 SHEET 3 A 3 SER A 120H THR A 120K-1 O VAL A 120J N VAL A 120B SHEET 1 B 8 SER A 40 SER A 43 0 SHEET 2 B 8 GLU A 32 ILE A 35 -1 N TYR A 33 O CYS A 42 SHEET 3 B 8 THR A 62 ILE A 66 -1 O ARG A 65 N SER A 34 SHEET 4 B 8 ALA A 82 VAL A 91 -1 O VAL A 84 N ALA A 64 SHEET 5 B 8 ARG A 103 LEU A 108 -1 O SER A 107 N THR A 87 SHEET 6 B 8 THR A 49 THR A 54 -1 N PHE A 52 O VAL A 106 SHEET 7 B 8 PHE A 45 ARG A 48A-1 N ARG A 48A O THR A 49 SHEET 8 B 8 SER A 241 LEU A 242 -1 O SER A 241 N THR A 48 SHEET 1 C 7 ALA A 135 GLY A 140 0 SHEET 2 C 7 GLY A 156 TYR A 171 -1 O GLY A 160 N VAL A 136 SHEET 3 C 7 GLY A 175 GLY A 183 -1 O LEU A 180 N VAL A 167 SHEET 4 C 7 SER A 226 ARG A 230 -1 O SER A 226 N GLY A 183 SHEET 5 C 7 ALA A 209 GLY A 216 -1 N GLY A 215 O LEU A 227 SHEET 6 C 7 SER A 198 ILE A 200 -1 N TRP A 199 O GLN A 210 SHEET 7 C 7 ALA A 135 GLY A 140 -1 N CYS A 137 O ILE A 200 SSBOND 1 CYS A 42 CYS A 58 1555 1555 2.06 SSBOND 2 CYS A 137 CYS A 159 1555 1555 2.04 SSBOND 3 CYS A 189 CYS A 220A 1555 1555 2.06 LINK OG SER A 195 B B2V B 203 1555 1555 1.47 LINK C1 AMSU B 199 N AALA B 200 1555 1555 1.33 LINK C1 BMSU B 199 N BALA B 200 1555 1555 1.36 LINK C PRO B 202 N B2V B 203 1555 1555 1.33 CISPEP 1 PHE A 94 PRO A 95 0 -6.10 SITE 1 AC1 11 ALA A 15A ASN A 15B ARG A 230 PRO A 233 SITE 2 AC1 11 HOH A 309 HOH A 334 HOH A 339 HOH A 374 SITE 3 AC1 11 HOH A 379 HOH A 398 HOH A 407 SITE 1 AC2 7 ALA A 169 ASN A 170 MSU B 199 ALA B 200 SITE 2 AC2 7 HOH B 409 HOH B 602 HOH B 711 SITE 1 AC3 6 ARG A 90 HOH A 318 HOH A 372 HOH A 377 SITE 2 AC3 6 HOH A 480 HOH A 603 SITE 1 AC4 15 LEU A 41 THR A 125 ARG A 141 SO4 A 249 SITE 2 AC4 15 HOH A 324 HOH A 357 HOH A 566 HOH A 593 SITE 3 AC4 15 HOH A 616 HOH A 617 HOH A 623 HOH A 640 SITE 4 AC4 15 HOH A 649 HOH A 705 HOH A 719 SITE 1 AC5 14 SER A 120G GLY A 123 SER A 124 THR A 125 SITE 2 AC5 14 ARG A 192 SO4 A 248 HOH A 332 HOH A 343 SITE 3 AC5 14 HOH A 357 HOH A 578 HOH A 616 HOH A 625 SITE 4 AC5 14 HOH A 641 HOH A 649 SITE 1 AC6 7 THR A 168 ARG A 178 HOH A 415 HOH A 513 SITE 2 AC6 7 HOH A 646 HOH A 650 HOH A 706 SITE 1 AC7 13 ALA A 48C THR A 49 SER A 110 ALA A 176 SITE 2 AC7 13 ARG A 178 HOH A 323 HOH A 344 HOH A 361 SITE 3 AC7 13 HOH A 463 HOH A 599 HOH A 613 HOH A 658 SITE 4 AC7 13 HOH A 707 SITE 1 AC8 8 ALA A 131 VAL A 132 LYS A 165 HOH A 472 SITE 2 AC8 8 HOH A 533 HOH A 591 HOH A 609 HOH A 670 SITE 1 AC9 16 LEU A 41 CYS A 42 HIS A 57 GLY A 193 SITE 2 AC9 16 SER A 195 GLN A 208 HOH A 393 HOH A 520 SITE 3 AC9 16 HOH A 582 HOH A 642 PRO B 202 B2V B 203 SITE 4 AC9 16 HOH B 378 HOH B 519 HOH B 589 HOH B 654 SITE 1 BC1 29 HIS A 57 ARG A 122 TYR A 171 GLY A 191 SITE 2 BC1 29 GLY A 193 ASP A 194 SER A 195 MET A 213 SITE 3 BC1 29 SER A 214 GLY A 215 GLY A 216 ASN A 217 SITE 4 BC1 29 VAL A 218 GLN A 219 GLY A 245 HOH A 382 SITE 5 BC1 29 HOH A 572 HOH A 585 HOH A 587 HOH A 642 SITE 6 BC1 29 HOH A 688 HOH A 715 HOH A 730 GOL B 204 SITE 7 BC1 29 SO4 B 208 HOH B 483 HOH B 654 HOH B 695 SITE 8 BC1 29 HOH B 711 CRYST1 65.768 65.768 79.554 90.00 90.00 120.00 P 32 2 1 6 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.015205 0.008779 0.000000 0.00000 SCALE2 0.000000 0.017557 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012570 0.00000