PDB Short entry for 2UUJ HEADER HYDROLASE/HYDROLASE INHIBITOR 03-MAR-07 2UUJ TITLE THROMBIN-HIRUGEN-GW473178 TERNARY COMPLEX AT 1.32A 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: PROTHROMBIN; 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, SERINE PROTEASE KEYWDS 2 INHIBITOR, HIRUGEN, ZYMOGEN, THROMBIN, PROTEASE, SULFATION, HIGH KEYWDS 3 RESOLUTION, SERINE PROTEINASE, BLOOD COAGULATION, PROTEASE KEYWDS 4 INHIBITOR, NON-COVALENT ACTIVE SITE INHIBITOR, HYDROLASE-HYDROLASE KEYWDS 5 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 8 13-DEC-23 2UUJ 1 REMARK LINK REVDAT 7 22-MAY-19 2UUJ 1 REMARK LINK REVDAT 6 07-AUG-13 2UUJ 1 REMARK REVDAT 5 13-JUL-11 2UUJ 1 VERSN REVDAT 4 24-FEB-09 2UUJ 1 VERSN REVDAT 3 05-AUG-08 2UUJ 1 REMARK REVDAT 2 25-SEP-07 2UUJ 1 FORMUL HETATM ANISOU CONECT REVDAT 1 04-SEP-07 2UUJ 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. 1.32 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) : 1.32 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.78 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 86.9 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) : 0.153 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.211 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 3524 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 71295 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)) : 0.147 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.202 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 2805 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 54732 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 : 28 REMARK 3 SOLVENT ATOMS : 337 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 2720.5 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 2289.0 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 14 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 25014 REMARK 3 NUMBER OF RESTRAINTS : 30856 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.017 REMARK 3 ANGLE DISTANCES (A) : 0.031 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.028 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.071 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.068 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.028 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.021 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.058 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.087 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: ASN60G IN CHAIN B IS GLYCOSYLATED. THE REMARK 3 COORDINATES LIST BELOW HAS AMINO ACID NUMBERING FOLLOWING THE REMARK 3 CHYMOTRYPSINOGEN NUMBERING SCHEME I.E. A MIXTURE OF SEQUENTIAL REMARK 3 NUMBERS AND ALPHABETICAL LETTERS. ASN60G IN CHAIN B IS REMARK 3 GLYCOSYLATED. THE MODEL WAS REFINED AGAINST F IN REFMAC-5, THEN REMARK 3 FINALLY REFINED IN SHELXL-97. HYDROGENS HAVE BEEN ADDED IN REMARK 3 RIDING POSITIONS. REMARK 4 REMARK 4 2UUJ 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_1290031657. 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 : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SRS REMARK 200 BEAMLINE : PX10.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.37 REMARK 200 MONOCHROMATOR : SI (1,1,1) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 71295 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.320 REMARK 200 RESOLUTION RANGE LOW (A) : 35.780 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 86.9 REMARK 200 DATA REDUNDANCY : 5.700 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.7500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.32 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.39 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 0.36000 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: STARTING MODEL IS A THROMBIN-HIRUGEN BINARY COMPLEX REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.32 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 35.02450 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.79000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 35.02450 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 35.79000 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: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4460 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12880 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -29.0 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 B2087 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: 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 SER B 37 C SER B 37 O 0.154 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 B 50 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 ARG B 67 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG B 75 CD - NE - CZ ANGL. DEV. = 12.8 DEGREES REMARK 500 ARG B 75 NE - CZ - NH1 ANGL. DEV. = 5.8 DEGREES REMARK 500 HIS B 91 CB - CG - CD2 ANGL. DEV. = 9.1 DEGREES REMARK 500 HIS B 91 CG - ND1 - CE1 ANGL. DEV. = 8.4 DEGREES REMARK 500 PRO B 92 O - C - N ANGL. DEV. = -13.0 DEGREES REMARK 500 ARG B 97 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG B 97 NE - CZ - NH2 ANGL. DEV. = -5.2 DEGREES REMARK 500 CYS B 182 CA - CB - SG ANGL. DEV. = 10.6 DEGREES REMARK 500 ARG B 206 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG B 206 NE - CZ - NH2 ANGL. DEV. = -5.0 DEGREES REMARK 500 ARG B 221 NE - CZ - NH1 ANGL. DEV. = 3.8 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 -86.39 -128.51 REMARK 500 CYS B 42 -170.27 174.61 REMARK 500 TYR B 60A 84.03 -158.33 REMARK 500 ASN B 60G 86.38 -160.47 REMARK 500 HIS B 71 -57.48 -133.14 REMARK 500 ILE B 79 -58.11 -130.31 REMARK 500 ASN B 95 76.66 -101.14 REMARK 500 ASN B 98 16.56 -141.36 REMARK 500 SER B 214 -116.13 -112.03 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 SER B 37 -13.73 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 B2001 DISTANCE = 6.03 ANGSTROMS REMARK 525 HOH B2003 DISTANCE = 6.08 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 CA B1249 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS B 169 O REMARK 620 2 THR B 172 O 85.3 REMARK 620 3 PHE B 204A O 99.8 100.1 REMARK 620 4 HOH B2200 O 72.9 78.6 172.6 REMARK 620 5 HOH B2240 O 177.6 96.5 81.3 106.0 REMARK 620 6 HOH B2243 O 86.7 171.5 78.5 101.7 91.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B1248 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ARG B 221 O REMARK 620 2 LYS B 224 O 93.5 REMARK 620 3 HOH B2212 O 87.3 94.5 REMARK 620 4 HOH B2215 O 163.3 74.0 82.9 REMARK 620 5 HOH B2227 O 97.6 83.0 174.6 91.8 REMARK 620 6 HOH B2259 O 105.6 160.9 85.0 87.0 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 1248 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 1249 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 896 B 1250 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: 2UUK RELATED DB: PDB REMARK 900 THROMBIN-HIRUGEN-GW420128 TERNARY COMPLEX AT 1.39A RESOLUTION REMARK 999 REMARK 999 SEQUENCE REMARK 999 RESIDUES THAT ARE MISSING FROM CHAIN A ARE THR1H-ALA1B AND REMARK 999 ARG15 REMARK 999 RESIDUES THAT ARE MISSING FROM CHAIN B ARE THR147-THR149 DBREF 2UUJ A 1H 15 UNP P00734 THRB_HUMAN 328 363 DBREF 2UUJ B 16 247 UNP P00734 THRB_HUMAN 364 622 DBREF 2UUJ 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 2UUJ TYS H 63 TYR O-SULFO-L-TYROSINE HET TYS H 63 16 HET NA B1248 1 HET CA B1249 1 HET 896 B1250 26 HETNAM TYS O-SULFO-L-TYROSINE HETNAM NA SODIUM ION HETNAM CA CALCIUM ION HETNAM 896 N-ETHYL-N-ISOPROPYL-3-METHYL-5-{[(2S)-2-(PYRIDIN-4- HETNAM 2 896 YLAMINO)PROPYL]OXY}BENZAMIDE FORMUL 3 TYS C9 H11 N O6 S FORMUL 4 NA NA 1+ FORMUL 5 CA CA 2+ FORMUL 6 896 C21 H29 N3 O2 FORMUL 7 HOH *337(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 2.05 SSBOND 2 CYS B 42 CYS B 58 1555 1555 2.07 SSBOND 3 CYS B 168 CYS B 182 1555 1555 2.04 SSBOND 4 CYS B 191 CYS B 220 1555 1555 2.13 LINK C GLU H 62 N TYS H 63 1555 1555 1.33 LINK C TYS H 63 N LEU H 64 1555 1555 1.34 LINK O LYS B 169 CA CA B1249 1555 1555 2.28 LINK O THR B 172 CA CA B1249 1555 1555 2.24 LINK O PHE B 204A CA CA B1249 4546 1555 2.37 LINK O ARG B 221 NA NA B1248 1555 1555 2.38 LINK O LYS B 224 NA NA B1248 1555 1555 2.33 LINK NA NA B1248 O HOH B2212 1555 1555 2.60 LINK NA NA B1248 O HOH B2215 1555 1555 2.43 LINK NA NA B1248 O HOH B2227 1555 1555 2.33 LINK NA NA B1248 O HOH B2259 1555 1555 2.40 LINK CA CA B1249 O HOH B2200 1555 1555 2.87 LINK CA CA B1249 O HOH B2240 1555 4546 2.43 LINK CA CA B1249 O HOH B2243 1555 4546 2.34 CISPEP 1 SER B 37 PRO B 37A 0 -11.20 SITE 1 AC1 6 ARG B 221 LYS B 224 HOH B2212 HOH B2215 SITE 2 AC1 6 HOH B2227 HOH B2259 SITE 1 AC2 6 LYS B 169 THR B 172 PHE B 204A HOH B2200 SITE 2 AC2 6 HOH B2240 HOH B2243 SITE 1 AC3 16 TYR B 60A TRP B 60D GLU B 97A LEU B 99 SITE 2 AC3 16 ILE B 174 ASP B 189 ALA B 190 CYS B 191 SITE 3 AC3 16 SER B 195 VAL B 213 SER B 214 TRP B 215 SITE 4 AC3 16 GLY B 216 GLY B 226 HOH B2266 HOH B2284 SITE 1 AC4 17 PHE B 34 GLN B 38 LEU B 65 ARG B 73 SITE 2 AC4 17 THR B 74 ARG B 75 TYR B 76 GLU B 80 SITE 3 AC4 17 LYS B 81 ILE B 82 MET B 84 HOH B2044 SITE 4 AC4 17 HOH B2085 HOH B2086 HOH H2001 HOH H2002 SITE 5 AC4 17 HOH H2003 CRYST1 70.049 71.580 72.052 90.00 100.31 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 0.014276 0.000000 0.002597 0.00000 SCALE2 0.000000 0.013970 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014107 0.00000