HEADER BLOOD CLOTTING/HYDROLASE INHIBITOR 31-JAN-05 1YPL TITLE X-RAY CRYSTAL STRUCTURE OF THROMBIN INHIBITED BY SYNTHETIC TITLE 2 CYANOPEPTIDE ANALOGUE RA-1008 COMPND MOL_ID: 1; COMPND 2 MOLECULE: THROMBIN LIGHT CHAIN; COMPND 3 CHAIN: L; COMPND 4 SYNONYM: COAGULATION FACTOR II; COMPND 5 EC: 3.4.21.5; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: THROMBIN HEAVY CHAIN; COMPND 8 CHAIN: H; COMPND 9 SYNONYM: COAGULATION FACTOR II; COMPND 10 EC: 3.4.21.5; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: HIRUDIN; COMPND 13 CHAIN: I; COMPND 14 FRAGMENT: RESIDUES 1-10; COMPND 15 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 TISSUE: BLOOD; 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; SOURCE 11 MOL_ID: 3; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: HIRUDO MEDICINALIS; SOURCE 14 ORGANISM_TAXID: 6421; SOURCE 15 OTHER_DETAILS: CHEMICALLY SYNTHESIZED KEYWDS THROMBIN, INHIBITOR COMPLEX, BARREL, 6 STRANDED BETA-SHEET, BLOOD KEYWDS 2 CLOTTING-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.FOKKENS,G.RADAU REVDAT 8 11-OCT-17 1YPL 1 REMARK REVDAT 7 13-NOV-13 1YPL 1 ATOM REVDAT 6 06-JUN-12 1YPL 1 REMARK REVDAT 5 13-JUL-11 1YPL 1 VERSN REVDAT 4 24-FEB-09 1YPL 1 VERSN REVDAT 3 06-MAR-07 1YPL 1 JRNL REVDAT 2 13-JUN-06 1YPL 1 JRNL REVDAT 1 17-JAN-06 1YPL 0 JRNL AUTH G.RADAU,J.FOKKENS JRNL TITL DESIGN AND X-RAY CRYSTAL STRUCTURES OF HUMAN THROMBIN WITH JRNL TITL 2 SYNTHETIC CYANOPEPTIDE-ANALOGUES. JRNL REF PHARMAZIE V. 62 83 2007 JRNL REFN ISSN 0031-7144 JRNL PMID 17341023 REMARK 2 REMARK 2 RESOLUTION. 1.85 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) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 86.9 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) : 0.195 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.195 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.263 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 2895 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 28802 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.185 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 21337 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2324 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 48 REMARK 3 SOLVENT ATOMS : 191 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 2534.0 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 2260.7 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 0 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 10263 REMARK 3 NUMBER OF RESTRAINTS : 9784 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.017 REMARK 3 ANGLE DISTANCES (A) : 0.025 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.026 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.034 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.045 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.058 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.000 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.077 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.000 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH & HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: ANISOTROPIC SCALING APPLIED BY THE REMARK 3 METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56, THE REMARK 3 FILE CONTAINS FRIEDEL PAIRS, THE BOND LENGTH BETWEEN C AND OXT REMARK 3 IN ILE(L 14K) IS SLIGHTLY LONG. REMARK 4 REMARK 4 1YPL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-FEB-05. REMARK 100 THE DEPOSITION ID IS D_1000031784. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-JAN-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU300 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : OSMIC MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : R-AXIS REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25907 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 1.800 REMARK 200 R MERGE (I) : 0.09900 REMARK 200 R SYM (I) : 0.09900 REMARK 200 FOR THE DATA SET : 9.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.88 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 1.80 REMARK 200 R MERGE FOR SHELL (I) : 0.44400 REMARK 200 R SYM FOR SHELL (I) : 0.44400 REMARK 200 FOR SHELL : 2.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: THE FILE CONTAINS FRIEDEL PAIRS. REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.65 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.44 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PHOSPHATE BUFFER, SODIUM CHLORIDE, PEG REMARK 280 8000, PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K 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 35.06550 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.81500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 35.06550 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 35.81500 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 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: L, H, I 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 CZ ARG H 75 LIES ON A SPECIAL POSITION. REMARK 375 HOH H9060 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 TRP H 147A REMARK 465 THR H 147B REMARK 465 ALA H 147C REMARK 465 ASN H 147D REMARK 465 VAL H 147E REMARK 465 GLY H 147F REMARK 465 LYS H 147G 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 LYS L 14A CG CD CE NZ REMARK 470 GLU H 127 CG CD OE1 OE2 REMARK 470 GLU I 4 CG CD OE1 OE2 REMARK 470 GLU I 7 CG CD OE1 OE2 REMARK 470 GLU I 8 CG CD OE1 OE2 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 ILE L 14K C ILE L 14K OXT 0.784 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 CYS L 1 CA - CB - SG ANGL. DEV. = 7.0 DEGREES REMARK 500 ILE L 14K C - N - CA ANGL. DEV. = 52.3 DEGREES REMARK 500 ARG H 75 NE - CZ - NH1 ANGL. DEV. = -3.1 DEGREES REMARK 500 HIS H 91 CB - CG - CD2 ANGL. DEV. = 7.6 DEGREES REMARK 500 TYR H 117 CB - CG - CD1 ANGL. DEV. = -3.8 DEGREES REMARK 500 ARG H 165 NE - CZ - NH1 ANGL. DEV. = -3.4 DEGREES REMARK 500 ARG H 173 NE - CZ - NH2 ANGL. DEV. = 3.0 DEGREES REMARK 500 ARG H 206 NE - CZ - NH1 ANGL. DEV. = -3.5 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 L 7 -83.68 -129.71 REMARK 500 GLN H 38 96.00 -57.01 REMARK 500 TYR H 60A 78.65 -160.53 REMARK 500 ASN H 60G 81.28 -152.77 REMARK 500 HIS H 71 -62.54 -126.31 REMARK 500 ILE H 79 -60.38 -126.65 REMARK 500 GLU H 97A -66.80 -120.22 REMARK 500 SER H 195 132.88 -34.91 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 TYR L 14J ILE L 14K -87.86 REMARK 500 REMARK 500 REMARK: NULL 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 H7777 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ARG H 221A O REMARK 620 2 HOH H9100 O 109.5 REMARK 620 3 HOH H9053 O 94.2 97.6 REMARK 620 4 LYS H 224 O 94.4 156.1 80.7 REMARK 620 5 HOH H9048 O 160.3 88.7 90.7 67.5 REMARK 620 6 HOH H9096 O 92.0 89.4 168.5 89.2 80.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA H7778 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS H 169 O REMARK 620 2 THR H 172 O 78.6 REMARK 620 3 HOH H9095 O 83.5 161.5 REMARK 620 4 PHE H 204A O 103.6 100.8 87.6 REMARK 620 5 HOH H9065 O 169.5 98.8 98.1 86.8 REMARK 620 6 HOH H9067 O 65.8 74.2 94.5 168.8 103.7 REMARK 620 N 1 2 3 4 5 REMARK 630 REMARK 630 MOLECULE TYPE: NULL REMARK 630 MOLECULE NAME: N-(BENZYLSULFONYL)-L-LEUCYL-N-(4-{[AMINO(IMINO) REMARK 630 METHYL]AMINO}BUTYL)-L-PROLINAMIDE REMARK 630 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 630 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 630 REMARK 630 M RES C SSSEQI REMARK 630 RA8 H 5555 REMARK 630 SOURCE: NULL REMARK 630 TAXONOMY: NULL REMARK 630 SUBCOMP: PMS LEU PRO AG2 REMARK 630 DETAILS: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA H 7777 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA H 7778 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE RA8 H 5555 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL H 6666 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL H 6667 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN I OF HIRUDIN REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1YPM RELATED DB: PDB REMARK 900 THE SAME PORTEIN COMPLEXED WITH RA-1014 DBREF 1YPL L 1B 14K UNP P00734 THRB_HUMAN 334 360 DBREF 1YPL H 16 245 UNP P00734 THRB_HUMAN 364 620 DBREF 1YPL I 1 10 UNP P28504 HIR2_HIRME 55 64 SEQRES 1 L 27 ALA ASP CYS GLY LEU ARG PRO LEU PHE GLU LYS LYS SER SEQRES 2 L 27 LEU GLU ASP LYS THR GLU ARG GLU LEU LEU GLU SER TYR SEQRES 3 L 27 ILE SEQRES 1 H 257 ILE VAL GLU GLY SER ASP ALA GLU ILE GLY MET SER PRO SEQRES 2 H 257 TRP GLN VAL MET LEU PHE ARG LYS SER PRO GLN GLU LEU SEQRES 3 H 257 LEU CYS GLY ALA SER LEU ILE SER ASP ARG TRP VAL LEU SEQRES 4 H 257 THR ALA ALA HIS CYS LEU LEU TYR PRO PRO TRP ASP LYS SEQRES 5 H 257 ASN PHE THR GLU ASN ASP LEU LEU VAL ARG ILE GLY LYS SEQRES 6 H 257 HIS SER ARG THR ARG TYR GLU ARG ASN ILE GLU LYS ILE SEQRES 7 H 257 SER MET LEU GLU LYS ILE TYR ILE HIS PRO ARG TYR ASN SEQRES 8 H 257 TRP ARG GLU ASN LEU ASP ARG ASP ILE ALA LEU MET LYS SEQRES 9 H 257 LEU LYS LYS PRO VAL ALA PHE SER ASP TYR ILE HIS PRO SEQRES 10 H 257 VAL CYS LEU PRO ASP ARG GLU THR ALA ALA SER LEU LEU SEQRES 11 H 257 GLN ALA GLY TYR LYS GLY ARG VAL THR GLY TRP GLY ASN SEQRES 12 H 257 LEU LYS GLU THR TRP THR ALA ASN VAL GLY LYS GLY GLN SEQRES 13 H 257 PRO SER VAL LEU GLN VAL VAL ASN LEU PRO ILE VAL GLU SEQRES 14 H 257 ARG PRO VAL CYS LYS ASP SER THR ARG ILE ARG ILE THR SEQRES 15 H 257 ASP ASN MET PHE CYS ALA GLY TYR LYS PRO ASP GLU GLY SEQRES 16 H 257 LYS ARG GLY ASP ALA CYS GLU GLY ASP SER GLY GLY PRO SEQRES 17 H 257 PHE VAL MET LYS SER PRO PHE ASN ASN ARG TRP TYR GLN SEQRES 18 H 257 MET GLY ILE VAL SER TRP GLY GLU GLY CYS ASP ARG ASP SEQRES 19 H 257 GLY LYS TYR GLY PHE TYR THR HIS VAL PHE ARG LEU LYS SEQRES 20 H 257 LYS TRP ILE GLN LYS VAL ILE ASP GLN PHE SEQRES 1 I 10 ASP PHE GLU GLU ILE PRO GLU GLU TYS LEU MODRES 1YPL TYS I 9 TYR O-SULFO-L-TYROSINE HET TYS I 9 16 HET NA H7777 1 HET NA H7778 1 HET RA8 H5555 34 HET GOL H6666 6 HET GOL H6667 6 HETNAM TYS O-SULFO-L-TYROSINE HETNAM NA SODIUM ION HETNAM RA8 N-(BENZYLSULFONYL)-L-LEUCYL-N-(4-{[AMINO(IMINO) HETNAM 2 RA8 METHYL]AMINO}BUTYL)-L-PROLINAMIDE HETNAM GOL GLYCEROL HETSYN RA8 1-GUANIDINO-4-(N-PHENYLMETHANESULFONYL-L-LEUCYL-L- HETSYN 2 RA8 PROLYLAMINO)BUTANE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 TYS C9 H11 N O6 S FORMUL 4 NA 2(NA 1+) FORMUL 6 RA8 C23 H38 N6 O4 S FORMUL 7 GOL 2(C3 H8 O3) FORMUL 9 HOH *191(H2 O) HELIX 1 1 PHE L 7 SER L 11 5 5 HELIX 2 2 THR L 14B TYR L 14J 1 9 HELIX 3 3 ALA H 55 CYS H 58 5 4 HELIX 4 4 PRO H 60B ASP H 60E 5 4 HELIX 5 5 THR H 60I ASN H 62 5 3 HELIX 6 6 ASP H 125 LEU H 130 1 9 HELIX 7 7 GLU H 164 SER H 171 1 8 HELIX 8 8 LYS H 185 GLY H 186C 5 5 HELIX 9 9 LEU H 234 PHE H 245 1 12 HELIX 10 10 PRO I 6 LEU I 10 5 5 SHEET 1 A 7 SER H 20 ASP H 21 0 SHEET 2 A 7 GLN H 156 PRO H 161 -1 O VAL H 157 N SER H 20 SHEET 3 A 7 LYS H 135 GLY H 140 -1 N GLY H 136 O LEU H 160 SHEET 4 A 7 PRO H 198 LYS H 202 -1 O VAL H 200 N ARG H 137 SHEET 5 A 7 TRP H 207 TRP H 215 -1 O TYR H 208 N MET H 201 SHEET 6 A 7 GLY H 226 HIS H 230 -1 O PHE H 227 N TRP H 215 SHEET 7 A 7 MET H 180 ALA H 183 -1 N PHE H 181 O TYR H 228 SHEET 1 B 7 LYS H 81 SER H 83 0 SHEET 2 B 7 LEU H 64 ILE H 68 -1 N ILE H 68 O LYS H 81 SHEET 3 B 7 GLN H 30 ARG H 35 -1 N MET H 32 O ARG H 67 SHEET 4 B 7 GLU H 39 LEU H 46 -1 O GLU H 39 N ARG H 35 SHEET 5 B 7 TRP H 51 THR H 54 -1 O LEU H 53 N SER H 45 SHEET 6 B 7 ALA H 104 LEU H 108 -1 O ALA H 104 N THR H 54 SHEET 7 B 7 LEU H 85 ILE H 90 -1 N LYS H 87 O LYS H 107 SHEET 1 C 2 LEU H 60 TYR H 60A 0 SHEET 2 C 2 LYS H 60F ASN H 60G-1 O LYS H 60F N TYR H 60A SSBOND 1 CYS L 1 CYS H 122 1555 1555 2.05 SSBOND 2 CYS H 42 CYS H 58 1555 1555 2.04 SSBOND 3 CYS H 168 CYS H 182 1555 1555 2.01 SSBOND 4 CYS H 191 CYS H 220 1555 1555 2.03 LINK NA NA H7777 O ARG H 221A 1555 1555 2.15 LINK NA NA H7777 O HOH H9100 1555 1555 2.21 LINK NA NA H7777 O HOH H9053 1555 1555 2.30 LINK NA NA H7777 O LYS H 224 1555 1555 2.41 LINK NA NA H7778 O LYS H 169 1555 1555 2.33 LINK NA NA H7778 O THR H 172 1555 1555 2.28 LINK NA NA H7778 O HOH H9095 1555 1555 2.57 LINK C GLU I 8 N TYS I 9 1555 1555 1.32 LINK C TYS I 9 N LEU I 10 1555 1555 1.32 LINK NA NA H7778 O PHE H 204A 1555 4546 2.30 LINK NA NA H7778 O HOH H9065 1555 4546 2.37 LINK NA NA H7777 O HOH H9048 1555 1555 2.78 LINK NA NA H7777 O HOH H9096 1555 1555 2.65 LINK NA NA H7778 O HOH H9067 1555 1555 2.88 CISPEP 1 SER H 36A PRO H 37 0 -6.51 SITE 1 AC1 6 ARG H 221A LYS H 224 HOH H9048 HOH H9053 SITE 2 AC1 6 HOH H9096 HOH H9100 SITE 1 AC2 6 LYS H 169 THR H 172 PHE H 204A HOH H9065 SITE 2 AC2 6 HOH H9067 HOH H9095 SITE 1 AC3 18 HIS H 57 TYR H 60A TRP H 60D GLU H 97A SITE 2 AC3 18 LEU H 99 ILE H 174 ASP H 189 ALA H 190 SITE 3 AC3 18 SER H 195 SER H 214 TRP H 215 GLY H 216 SITE 4 AC3 18 GLU H 217 GLY H 219 GLY H 226 HOH H9001 SITE 5 AC3 18 HOH H9028 HOH H9046 SITE 1 AC4 2 ASN H 60G HOH H9075 SITE 1 AC5 5 ARG H 97 ASN H 205 HOH H9041 LEU L 3 SITE 2 AC5 5 GLU L 8 SITE 1 AC6 12 PHE H 34 LEU H 65 ARG H 67 ARG H 73 SITE 2 AC6 12 THR H 74 TYR H 76 GLU H 80 LYS H 81 SITE 3 AC6 12 ILE H 82 HOH H9019 HOH I9111 HOH I9160 CRYST1 70.131 71.630 72.198 90.00 100.45 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 0.014259 0.000000 0.002630 0.00000 SCALE2 0.000000 0.013961 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014084 0.00000