PDB Short entry for 2UUK HEADER HYDROLASE/HYDROLASE INHIBITOR 03-MAR-07 2UUK TITLE THROMBIN-HIRUGEN-GW420128 TERNARY COMPLEX AT 1.39A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: HUMAN ALPHA THROMBIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 328-363; COMPND 5 EC: 3.4.21.5; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: THROMBIN; COMPND 8 CHAIN: B; COMPND 9 FRAGMENT: RESIDUES 364-622; COMPND 10 SYNONYM: HUMAN ALPHA THROMBIN, COAGULATION FACTOR II; COMPND 11 EC: 3.4.21.5; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: HIRUDIN I; COMPND 14 CHAIN: H; COMPND 15 FRAGMENT: RESIDUES 55-64; COMPND 16 SYNONYM: HIRUGEN; COMPND 17 ENGINEERED: YES; COMPND 18 OTHER_DETAILS: EXOSITE I INHIBITOR OF THROMBIN SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 TISSUE: BLOOD PLASMA; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 8 ORGANISM_COMMON: HUMAN; SOURCE 9 ORGANISM_TAXID: 9606; SOURCE 10 TISSUE: BLOOD PLASMA; SOURCE 11 MOL_ID: 3; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: HIRUDO MEDICINALIS; SOURCE 14 ORGANISM_COMMON: MEDICINAL LEECH; SOURCE 15 ORGANISM_TAXID: 6421; SOURCE 16 OTHER_DETAILS: THIS POLYPEPTIDE CHAIN WAS CHEMICALLY SYNTHESIZED. SOURCE 17 THE SEQUENCE FOR THIS CHAIN OCCURS NATURALLY IN THE C-TERMINAL OF SOURCE 18 MEDICINAL LEECH(HIRUDO MEDICINALIS). KEYWDS BLOOD CLOTTING, GLYCOPROTEIN, SERINE PROTEASE, CLEAVAGE ON PAIR OF KEYWDS 2 BASIC RESIDUES, THROMBIN, SERINE PROTEASE INHIBITOR, HIRUGEN, KEYWDS 3 ZYMOGEN, PROTEASE, SULFATION, HIGH RESOLUTION, SERINE PROTEINASE, KEYWDS 4 BLOOD COAGULATION, PROTEASE INHIBITOR, NON-COVALENT ACTIVE SITE KEYWDS 5 INHIBITOR, HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR H.U.AHMED,M.P.BLAKELEY,M.CIANCI,D.W.J.CRUICKSHANK,J.A.HUBBARD, AUTHOR 2 J.R.HELLIWELL REVDAT 7 22-MAY-19 2UUK 1 REMARK LINK REVDAT 6 07-AUG-13 2UUK 1 REMARK ATOM REVDAT 5 13-JUL-11 2UUK 1 VERSN REVDAT 4 28-APR-09 2UUK 1 HETATM ANISOU REVDAT 3 24-FEB-09 2UUK 1 VERSN REVDAT 2 05-AUG-08 2UUK 1 REMARK REVDAT 1 04-SEP-07 2UUK 0 JRNL AUTH H.U.AHMED,M.P.BLAKELEY,M.CIANCI,D.W.J.CRUICKSHANK, JRNL AUTH 2 J.A.HUBBARD,J.R.HELLIWELL JRNL TITL THE DETERMINATION OF PROTONATION STATES IN PROTEINS. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 63 906 2007 JRNL REFN ISSN 0907-4449 JRNL PMID 17642517 JRNL DOI 10.1107/S0907444907029976 REMARK 2 REMARK 2 RESOLUTION. 1.39 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) : 1.39 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 18.55 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.9 REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE 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) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.118 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.173 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 3345 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 67018 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)) : 0.112 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.165 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 3345.0 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 2767 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 53556 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2360 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 35 REMARK 3 SOLVENT ATOMS : 345 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 2739.9 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 2233.9 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 10 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 25160 REMARK 3 NUMBER OF RESTRAINTS : 30942 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.012 REMARK 3 ANGLE DISTANCES (A) : 0.032 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.029 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.064 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.080 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.042 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.004 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.058 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.104 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE COORDINATES LIST BELOW HAS AMINO REMARK 3 ACID NUMBERING FOLLOWING THE CHYMOTRYPSINOGEN NUMBERING SCHEME REMARK 3 I.E. A MIXTURE OF SEQUENTIAL NUMBERS AND ALPHABETICAL LETTERS. REMARK 3 ASN60G IN CHAIN B IS GLYCOSYLATED. THE MODEL WAS INITIALLY REMARK 3 REFINED AGAINST F IN REFMAC-5, THEN FINALLY REFINED AGAINST REMARK 3 F(SQUARED) USING SHELXL-97. HYDROGENS HAVE BEEN ADDED IN RIDING REMARK 3 POSITIONS. REMARK 4 REMARK 4 2UUK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 03-MAR-07. REMARK 100 THE DEPOSITION ID IS D_1290031658. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 17-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00 REMARK 200 MONOCHROMATOR : SI (111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 67018 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.390 REMARK 200 RESOLUTION RANGE LOW (A) : 18.550 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.9 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.39 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.46 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.4 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : 0.34000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.320 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: REFMAC 5, SHELXL-97 REMARK 200 STARTING MODEL: PDB ENTRY 2UUF REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTALLIZATION CONDITIONS: CRYSTALS REMARK 280 WERE GROWN BY MACROSEEDING A SOLUTION OF 100MM HEPES PH 7.0, 28% REMARK 280 PEG4K,500MM NACL. REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z 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 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 35.17300 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.71800 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 35.17300 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 35.71800 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 TOTAL BURIED SURFACE AREA: 3910 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15820 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.1 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, H 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 B1104 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 THR A 1H REMARK 465 PHE A 1G REMARK 465 GLY A 1F REMARK 465 SER A 1E REMARK 465 GLY A 1D REMARK 465 GLU A 1C REMARK 465 GLY A 14M REMARK 465 ARG A 15 REMARK 465 TRP B 148 REMARK 465 THR B 149 REMARK 465 ALA B 149A REMARK 465 ASN B 149B REMARK 465 VAL B 149C REMARK 465 GLY B 149D REMARK 465 LYS B 149E REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 THR B 147 OG1 CG2 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 O HOH B 1074 O HOH B 1079 2.14 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 VAL B 157 C VAL B 158 N 0.178 REMARK 500 GLU B 247 C GLU B 247 O 1.568 REMARK 500 LEU H 64 C LEU H 64 O 0.335 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 4 NE - CZ - NH2 ANGL. DEV. = 3.2 DEGREES REMARK 500 LYS A 10 CA - CB - CG ANGL. DEV. = 17.7 DEGREES REMARK 500 ARG A 14D CD - NE - CZ ANGL. DEV. = 18.8 DEGREES REMARK 500 ARG A 14D NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 GLN B 30 CB - CG - CD ANGL. DEV. = 21.1 DEGREES REMARK 500 GLN B 30 OE1 - CD - NE2 ANGL. DEV. = -16.8 DEGREES REMARK 500 ARG B 35 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 ARG B 35 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 ARG B 50 CG - CD - NE ANGL. DEV. = 17.1 DEGREES REMARK 500 ARG B 75 NH1 - CZ - NH2 ANGL. DEV. = 9.3 DEGREES REMARK 500 ARG B 75 NE - CZ - NH1 ANGL. DEV. = -13.2 DEGREES REMARK 500 ARG B 75 NE - CZ - NH2 ANGL. DEV. = 4.0 DEGREES REMARK 500 HIS B 91 ND1 - CG - CD2 ANGL. DEV. = -9.9 DEGREES REMARK 500 HIS B 91 CG - ND1 - CE1 ANGL. DEV. = 14.4 DEGREES REMARK 500 HIS B 91 ND1 - CE1 - NE2 ANGL. DEV. = -8.9 DEGREES REMARK 500 PRO B 92 O - C - N ANGL. DEV. = -11.9 DEGREES REMARK 500 ARG B 93 C - N - CA ANGL. DEV. = 16.1 DEGREES REMARK 500 TYR B 94 CB - CG - CD2 ANGL. DEV. = -3.8 DEGREES REMARK 500 TYR B 94 CB - CG - CD1 ANGL. DEV. = 4.7 DEGREES REMARK 500 ARG B 101 NE - CZ - NH2 ANGL. DEV. = 5.5 DEGREES REMARK 500 ARG B 173 NE - CZ - NH1 ANGL. DEV. = -4.1 DEGREES REMARK 500 ARG B 187 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 ARG B 233 NE - CZ - NH2 ANGL. DEV. = -4.6 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 PHE A 7 -90.72 -129.12 REMARK 500 TYR B 60A 85.37 -157.41 REMARK 500 ASN B 60G 82.48 -159.92 REMARK 500 HIS B 71 -61.63 -130.76 REMARK 500 ILE B 79 -56.81 -125.24 REMARK 500 ASN B 98 14.05 -142.34 REMARK 500 SER B 214 -120.03 -109.58 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B1002 DISTANCE = 5.87 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B2248 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ARG B 221 O REMARK 620 2 LYS B 224 O 92.9 REMARK 620 3 HOH B1242 O 98.4 83.4 REMARK 620 4 HOH B1227 O 160.5 71.5 91.6 REMARK 620 5 HOH B1268 O 106.7 160.3 95.4 88.9 REMARK 620 6 HOH B1224 O 87.5 93.1 173.3 81.9 85.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B2249 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS B 169 O REMARK 620 2 HOH B1201 O 80.1 REMARK 620 3 PHE B 204A O 93.2 88.2 REMARK 620 4 THR B 172 O 86.3 166.0 89.3 REMARK 620 5 HOH B1252 O 171.0 108.9 86.3 84.7 REMARK 620 6 HOH B1212 O 83.2 100.0 170.3 81.5 95.8 REMARK 620 N 1 2 3 4 5 REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: DSSP REMARK 700 THE SHEETS PRESENTED AS "BB" IN EACH CHAIN ON SHEET RECORDS REMARK 700 BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY REMARK 700 A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS REMARK 700 ARE IDENTICAL. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 2248 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 2249 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 897 B 2250 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN H OF HIRUDIN I REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2UU8 RELATED DB: PDB REMARK 900 X-RAY STRUCTURE OF NI, CA CONCANAVALIN A AT ULTRA- HIGH RESOLUTION REMARK 900 (0.94A) REMARK 900 RELATED ID: 2UUF RELATED DB: PDB REMARK 900 THROMBIN-HIRUGEN BINARY COMPLEX AT 1.26A RESOLUTION REMARK 900 RELATED ID: 2UUJ RELATED DB: PDB REMARK 900 THROMBIN-HIRUGEN-GW473178 TERNARY COMPLEX AT 1.32A RESOLUTION REMARK 999 REMARK 999 SEQUENCE REMARK 999 RESIDUES THAT ARE MISSING FROM CHAIN A ARE THR1H-GLU1C AND REMARK 999 GLY14M-ARG15. REMARK 999 RESIDUES THAT ARE MISSING FROM CHAIN B ARE TRP148-LYS149E REMARK 999 TYR H 63 IS SULFONATED DBREF 2UUK A 1H 15 UNP P00734 THRB_HUMAN 328 363 DBREF 2UUK B 16 247 UNP P00734 THRB_HUMAN 364 622 DBREF 2UUK H 55 64 UNP P28501 ITHA_HIRME 55 64 SEQRES 1 A 36 THR PHE GLY SER GLY GLU ALA ASP CYS GLY LEU ARG PRO SEQRES 2 A 36 LEU PHE GLU LYS LYS SER LEU GLU ASP LYS THR GLU ARG SEQRES 3 A 36 GLU LEU LEU GLU SER TYR ILE ASP GLY ARG SEQRES 1 B 259 ILE VAL GLU GLY SER ASP ALA GLU ILE GLY MET SER PRO SEQRES 2 B 259 TRP GLN VAL MET LEU PHE ARG LYS SER PRO GLN GLU LEU SEQRES 3 B 259 LEU CYS GLY ALA SER LEU ILE SER ASP ARG TRP VAL LEU SEQRES 4 B 259 THR ALA ALA HIS CYS LEU LEU TYR PRO PRO TRP ASP LYS SEQRES 5 B 259 ASN PHE THR GLU ASN ASP LEU LEU VAL ARG ILE GLY LYS SEQRES 6 B 259 HIS SER ARG THR ARG TYR GLU ARG ASN ILE GLU LYS ILE SEQRES 7 B 259 SER MET LEU GLU LYS ILE TYR ILE HIS PRO ARG TYR ASN SEQRES 8 B 259 TRP ARG GLU ASN LEU ASP ARG ASP ILE ALA LEU MET LYS SEQRES 9 B 259 LEU LYS LYS PRO VAL ALA PHE SER ASP TYR ILE HIS PRO SEQRES 10 B 259 VAL CYS LEU PRO ASP ARG GLU THR ALA ALA SER LEU LEU SEQRES 11 B 259 GLN ALA GLY TYR LYS GLY ARG VAL THR GLY TRP GLY ASN SEQRES 12 B 259 LEU LYS GLU THR TRP THR ALA ASN VAL GLY LYS GLY GLN SEQRES 13 B 259 PRO SER VAL LEU GLN VAL VAL ASN LEU PRO ILE VAL GLU SEQRES 14 B 259 ARG PRO VAL CYS LYS ASP SER THR ARG ILE ARG ILE THR SEQRES 15 B 259 ASP ASN MET PHE CYS ALA GLY TYR LYS PRO ASP GLU GLY SEQRES 16 B 259 LYS ARG GLY ASP ALA CYS GLU GLY ASP SER GLY GLY PRO SEQRES 17 B 259 PHE VAL MET LYS SER PRO PHE ASN ASN ARG TRP TYR GLN SEQRES 18 B 259 MET GLY ILE VAL SER TRP GLY GLU GLY CYS ASP ARG ASP SEQRES 19 B 259 GLY LYS TYR GLY PHE TYR THR HIS VAL PHE ARG LEU LYS SEQRES 20 B 259 LYS TRP ILE GLN LYS VAL ILE ASP GLN PHE GLY GLU SEQRES 1 H 10 ASP PHE GLU GLU ILE PRO GLU GLU TYS LEU MODRES 2UUK TYS H 63 TYR O-SULFO-L-TYROSINE HET TYS H 63 16 HET NA B2248 1 HET CA B2249 1 HET 897 B2250 33 HETNAM TYS O-SULFO-L-TYROSINE HETNAM NA SODIUM ION HETNAM CA CALCIUM ION HETNAM 897 N-[3-(TERT-BUTYLAMINO)-3-OXOPROPYL]-N-ISOPROPYL-3- HETNAM 2 897 METHYL-5-{[(2S)-2-(PYRIDIN-4-YLAMINO) HETNAM 3 897 PROPYL]OXY}BENZAMIDE FORMUL 3 TYS C9 H11 N O6 S FORMUL 4 NA NA 1+ FORMUL 5 CA CA 2+ FORMUL 6 897 C26 H38 N4 O3 FORMUL 7 HOH *345(H2 O) HELIX 1 1 PHE A 7 SER A 11 5 5 HELIX 2 2 THR A 14B TYR A 14J 1 9 HELIX 3 3 ALA B 55 CYS B 58 5 4 HELIX 4 4 PRO B 60B ASP B 60E 5 4 HELIX 5 5 THR B 60I ASN B 62 5 3 HELIX 6 6 ASP B 125 LEU B 130 1 9 HELIX 7 7 GLU B 164 SER B 171 1 8 HELIX 8 8 LYS B 185 GLY B 186C 5 5 HELIX 9 9 LEU B 234 GLY B 246 1 13 SHEET 1 BA 7 SER B 20 ASP B 21 0 SHEET 2 BA 7 GLN B 156 PRO B 161 -1 O VAL B 157 N SER B 20 SHEET 3 BA 7 LYS B 135 GLY B 140 -1 O GLY B 136 N LEU B 160 SHEET 4 BA 7 PRO B 198 LYS B 202 -1 O PRO B 198 N THR B 139 SHEET 5 BA 7 TRP B 207 VAL B 213 -1 O TYR B 208 N MET B 201 SHEET 6 BA 7 GLY B 226 HIS B 230 -1 N THR B 229 O ILE B 212 SHEET 7 BA 7 MET B 180 ALA B 183 -1 O PHE B 181 N TYR B 228 SHEET 1 BB 7 LYS B 81 SER B 83 0 SHEET 2 BB 7 LEU B 64 ILE B 68 -1 O VAL B 66 N SER B 83 SHEET 3 BB 7 GLN B 30 ARG B 35 -1 O MET B 32 N ARG B 67 SHEET 4 BB 7 GLU B 39 LEU B 46 -1 O GLU B 39 N ARG B 35 SHEET 5 BB 7 TRP B 51 THR B 54 -1 O LEU B 53 N SER B 45 SHEET 6 BB 7 ALA B 104 LEU B 108 -1 O ALA B 104 N THR B 54 SHEET 7 BB 7 LEU B 85 ILE B 90 -1 N GLU B 86 O LYS B 107 SHEET 1 BC 2 LEU B 60 TYR B 60A 0 SHEET 2 BC 2 LYS B 60F ASN B 60G-1 O LYS B 60F N TYR B 60A SSBOND 1 CYS A 1 CYS B 122 1555 1555 2.08 SSBOND 2 CYS B 42 CYS B 58 1555 1555 2.09 SSBOND 3 CYS B 168 CYS B 182 1555 1555 2.06 SSBOND 4 CYS B 191 CYS B 220 1555 1555 2.16 LINK NA NA B2248 O ARG B 221 1555 1555 2.32 LINK NA NA B2248 O LYS B 224 1555 1555 2.37 LINK NA NA B2248 O HOH B1242 1555 1555 2.36 LINK NA NA B2248 O HOH B1227 1555 1555 2.45 LINK NA NA B2248 O HOH B1268 1555 1555 2.42 LINK CA CA B2249 O LYS B 169 1555 1555 2.30 LINK CA CA B2249 O HOH B1201 1555 1555 2.09 LINK CA CA B2249 O PHE B 204A 1555 4546 2.37 LINK CA CA B2249 O THR B 172 1555 1555 2.26 LINK CA CA B2249 O HOH B1252 1555 4546 2.25 LINK CA CA B2249 O HOH B1212 1555 1555 2.48 LINK C GLU H 62 N TYS H 63 1555 1555 1.33 LINK C TYS H 63 N LEU H 64 1555 1555 1.32 LINK NA NA B2248 O HOH B1224 1555 1555 2.65 CISPEP 1 SER B 37 PRO B 37A 0 -12.33 SITE 1 AC1 6 ARG B 221 LYS B 224 HOH B1224 HOH B1227 SITE 2 AC1 6 HOH B1242 HOH B1268 SITE 1 AC2 6 LYS B 169 THR B 172 PHE B 204A HOH B1201 SITE 2 AC2 6 HOH B1212 HOH B1252 SITE 1 AC3 18 HIS B 57 TYR B 60A TRP B 60D GLU B 97A SITE 2 AC3 18 ASP B 189 ALA B 190 CYS B 191 SER B 195 SITE 3 AC3 18 VAL B 213 SER B 214 TRP B 215 GLY B 216 SITE 4 AC3 18 GLY B 226 HOH B1278 HOH B1291 HOH B1292 SITE 5 AC3 18 HOH B1293 HOH B1294 SITE 1 AC4 22 PHE B 34 GLN B 38 LEU B 40 LEU B 65 SITE 2 AC4 22 ARG B 73 THR B 74 ARG B 75 TYR B 76 SITE 3 AC4 22 GLU B 80 LYS B 81 ILE B 82 HOH B1050 SITE 4 AC4 22 HOH B1051 HOH B1101 HOH B1116 HOH H1001 SITE 5 AC4 22 HOH H1002 HOH H1003 HOH H1004 HOH H1005 SITE 6 AC4 22 HOH H1006 HOH H1007 CRYST1 70.346 71.436 72.116 90.00 100.03 90.00 C 1 2 1 4 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 0.014215 0.000000 0.002514 0.00000 SCALE2 0.000000 0.013999 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014082 0.00000