HEADER HYDROLASE 16-APR-18 6GBW TITLE THROMBIN IN COMPLEX WITH MI2100 ((S)-N-(2-(AMINOMETHYL)-5- TITLE 2 CHLOROBENZYL)-1-((BENZYLSULFONYL)-L-ARGINYL)PYRROLIDINE-2- TITLE 3 CARBOXAMIDE) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTHROMBIN; 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: PROTHROMBIN; 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 VARIANT-2; COMPND 13 CHAIN: I; COMPND 14 ENGINEERED: YES; COMPND 15 OTHER_DETAILS: HTTP://SHOP.BACHEM.COM/H-7425.HTML CONTAINS SULFATED COMPND 16 TYROSINE 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_COMMON: MEDICINAL LEECH; SOURCE 15 ORGANISM_TAXID: 6421 KEYWDS COAGULATION, BLOOD CLOTTING, CONVERTION OF FIBRINOGEN TO FIBRIN, KEYWDS 2 BLOOD CLOTTING INHIBITOR, THROMBIN INHIBITOR, PREORGANIZATION, KEYWDS 3 GLYCOSYLATION, BLOOD, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR A.SANDNER,A.HEINE,G.KLEBE REVDAT 4 17-JAN-24 6GBW 1 HETSYN REVDAT 3 29-JUL-20 6GBW 1 COMPND REMARK HETNAM LINK REVDAT 3 2 1 SITE REVDAT 2 27-NOV-19 6GBW 1 JRNL REVDAT 1 24-APR-19 6GBW 0 JRNL AUTH A.SANDNER,T.HUFNER-WULSDORF,A.HEINE,T.STEINMETZER,G.KLEBE JRNL TITL STRATEGIES FOR LATE-STAGE OPTIMIZATION: PROFILING JRNL TITL 2 THERMODYNAMICS BY PREORGANIZATION AND SALT BRIDGE SHIELDING. JRNL REF J.MED.CHEM. V. 62 9753 2019 JRNL REFN ISSN 0022-2623 JRNL PMID 31633354 JRNL DOI 10.1021/ACS.JMEDCHEM.9B01196 REMARK 2 REMARK 2 RESOLUTION. 1.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 21.78 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 61497 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.134 REMARK 3 R VALUE (WORKING SET) : 0.132 REMARK 3 FREE R VALUE : 0.165 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3075 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 21.7866 - 4.0533 0.98 2700 142 0.1450 0.1601 REMARK 3 2 4.0533 - 3.2206 0.98 2658 140 0.1293 0.1685 REMARK 3 3 3.2206 - 2.8144 0.99 2667 140 0.1449 0.1661 REMARK 3 4 2.8144 - 2.5575 0.99 2685 141 0.1371 0.1632 REMARK 3 5 2.5575 - 2.3745 0.99 2631 139 0.1230 0.1612 REMARK 3 6 2.3745 - 2.2346 0.99 2700 142 0.1181 0.1547 REMARK 3 7 2.2346 - 2.1228 0.99 2654 140 0.1134 0.1524 REMARK 3 8 2.1228 - 2.0305 1.00 2659 140 0.1113 0.1434 REMARK 3 9 2.0305 - 1.9524 1.00 2691 141 0.1138 0.1428 REMARK 3 10 1.9524 - 1.8850 1.00 2673 141 0.1124 0.1690 REMARK 3 11 1.8850 - 1.8261 1.00 2655 140 0.1127 0.1494 REMARK 3 12 1.8261 - 1.7739 1.00 2661 140 0.1126 0.1653 REMARK 3 13 1.7739 - 1.7273 1.00 2634 138 0.1178 0.1724 REMARK 3 14 1.7273 - 1.6851 0.99 2694 142 0.1256 0.1577 REMARK 3 15 1.6851 - 1.6468 0.99 2641 139 0.1263 0.1618 REMARK 3 16 1.6468 - 1.6118 0.99 2642 139 0.1343 0.1596 REMARK 3 17 1.6118 - 1.5796 0.99 2665 140 0.1466 0.1888 REMARK 3 18 1.5796 - 1.5498 0.99 2621 138 0.1468 0.1853 REMARK 3 19 1.5498 - 1.5221 0.99 2640 139 0.1565 0.1752 REMARK 3 20 1.5221 - 1.4963 0.99 2647 140 0.1831 0.2337 REMARK 3 21 1.4963 - 1.4722 0.98 2624 138 0.2020 0.2227 REMARK 3 22 1.4722 - 1.4495 0.96 2580 136 0.2140 0.2765 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.130 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 15.550 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.008 2591 REMARK 3 ANGLE : 0.995 3529 REMARK 3 CHIRALITY : 0.081 366 REMARK 3 PLANARITY : 0.007 475 REMARK 3 DIHEDRAL : 22.171 1003 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: PHENIX REFINEMENT REMARK 4 REMARK 4 6GBW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-APR-18. REMARK 100 THE DEPOSITION ID IS D_1200009506. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-MAY-17 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 : BESSY REMARK 200 BEAMLINE : 14.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9184 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL REMARK 200 OPTICS : SAGITALLY BENDED SI111 CRYSTAL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 61523 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.450 REMARK 200 RESOLUTION RANGE LOW (A) : 43.431 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04500 REMARK 200 FOR THE DATA SET : 15.4100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.54 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.50000 REMARK 200 FOR SHELL : 2.340 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 1H8D REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.47 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20 MM SODIUM DIHYDROGEN PHOSPHATE PH REMARK 280 7.5 350 MM NACL 27% PEG 8000, VAPOR DIFFUSION, HANGING DROP, REMARK 280 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 34.92000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.55950 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 34.92000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 35.55950 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4170 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12510 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -31.0 KCAL/MOL 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 HOH H 404 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 L -4 REMARK 465 PHE L -3 REMARK 465 GLY L -2 REMARK 465 SER L -1 REMARK 465 GLY L 0 REMARK 465 ASP L 15 REMARK 465 GLY L 16 REMARK 465 ARG L 17 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 465 GLY H 246 REMARK 465 GLU H 247 REMARK 465 GLY I 517 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 GLU L 1C CG CD OE1 OE2 REMARK 470 LYS L 9 NZ REMARK 470 LYS L 14A NZ REMARK 470 SER H 36A OG REMARK 470 ARG H 50 CG CD NE CZ NH1 NH2 REMARK 470 ASN H 62 OD1 ND2 REMARK 470 MET H 84 CE REMARK 470 LYS H 87 CE NZ REMARK 470 LYS H 107 NZ REMARK 470 LYS H 110 CE NZ REMARK 470 THR H 147 OG1 CG2 REMARK 470 ASP H 186A CG OD1 OD2 REMARK 470 GLU H 192 CD OE1 OE2 REMARK 470 LYS H 236 CD CE NZ REMARK 470 GLN H 239 CG CD OE1 NE2 REMARK 470 LYS H 240 CD CE NZ REMARK 470 GLN H 244 CD OE1 NE2 REMARK 470 ASP I 518 CG OD1 OD2 REMARK 470 GLU I 521 CG CD OE1 OE2 REMARK 470 GLU I 524 CG CD OE1 OE2 REMARK 470 GLN I 528 CG CD OE1 NE2 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 HZ1 LYS L 10 O HOH L 101 1.55 REMARK 500 ND2 ASN H 60G C1 NAG H 301 1.62 REMARK 500 ND2 ASN H 60G O5 NAG H 301 2.17 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 -88.24 -130.16 REMARK 500 TYR H 60A 85.63 -154.17 REMARK 500 ASN H 60G 81.16 -156.35 REMARK 500 HIS H 71 -61.56 -129.29 REMARK 500 ILE H 79 -62.63 -126.57 REMARK 500 GLU H 97A -74.58 -117.32 REMARK 500 GLU H 97A -74.58 -112.47 REMARK 500 SER H 195 132.23 -37.06 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 H 599 DISTANCE = 5.85 ANGSTROMS REMARK 525 HOH H 600 DISTANCE = 6.25 ANGSTROMS REMARK 525 HOH H 601 DISTANCE = 6.48 ANGSTROMS 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 NAG H 301 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 H 302 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS H 169 O REMARK 620 2 THR H 172 O 82.6 REMARK 620 3 PHE H 204A O 17.9 92.7 REMARK 620 4 HOH H 462 O 68.4 80.0 55.6 REMARK 620 5 HOH H 507 O 174.0 95.1 158.1 105.8 REMARK 620 6 HOH H 540 O 83.1 165.6 73.9 96.3 99.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA H 303 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ARG H 221A O REMARK 620 2 LYS H 224 O 93.4 REMARK 620 3 HOH H 472 O 160.4 70.1 REMARK 620 4 HOH H 490 O 87.9 89.5 81.7 REMARK 620 5 HOH H 494 O 107.6 157.1 87.4 82.5 REMARK 620 6 HOH H 560 O 96.5 83.4 92.1 171.9 102.6 REMARK 620 N 1 2 3 4 5 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5JZY RELATED DB: PDB REMARK 900 SAME LIGAND SERIES REMARK 900 RELATED ID: 3RML RELATED DB: PDB REMARK 900 SAME LIGAND SERIES REMARK 900 RELATED ID: 5JFD RELATED DB: PDB REMARK 900 SAME LIGAND WITH D-ARGININE INSTEAD OF L-ARGININE REMARK 900 RELATED ID: 5LCE RELATED DB: PDB REMARK 900 SAME LIGAND SERIES REMARK 900 RELATED ID: 5LPD RELATED DB: PDB REMARK 900 SAME LIGAND SERIES DBREF 6GBW L -4 17 UNP P00734 THRB_HUMAN 328 363 DBREF 6GBW H 16 247 UNP P00734 THRB_HUMAN 364 622 DBREF 6GBW I 517 528 UNP P09945 HIRV2_HIRME 61 72 SEQRES 1 L 36 THR PHE GLY SER GLY GLU ALA ASP CYS GLY LEU ARG PRO SEQRES 2 L 36 LEU PHE GLU LYS LYS SER LEU GLU ASP LYS THR GLU ARG SEQRES 3 L 36 GLU LEU LEU GLU SER TYR ILE ASP GLY ARG SEQRES 1 H 259 ILE VAL GLU GLY SER ASP ALA GLU ILE GLY MET SER PRO SEQRES 2 H 259 TRP GLN VAL MET LEU PHE ARG LYS SER PRO GLN GLU LEU SEQRES 3 H 259 LEU CYS GLY ALA SER LEU ILE SER ASP ARG TRP VAL LEU SEQRES 4 H 259 THR ALA ALA HIS CYS LEU LEU TYR PRO PRO TRP ASP LYS SEQRES 5 H 259 ASN PHE THR GLU ASN ASP LEU LEU VAL ARG ILE GLY LYS SEQRES 6 H 259 HIS SER ARG THR ARG TYR GLU ARG ASN ILE GLU LYS ILE SEQRES 7 H 259 SER MET LEU GLU LYS ILE TYR ILE HIS PRO ARG TYR ASN SEQRES 8 H 259 TRP ARG GLU ASN LEU ASP ARG ASP ILE ALA LEU MET LYS SEQRES 9 H 259 LEU LYS LYS PRO VAL ALA PHE SER ASP TYR ILE HIS PRO SEQRES 10 H 259 VAL CYS LEU PRO ASP ARG GLU THR ALA ALA SER LEU LEU SEQRES 11 H 259 GLN ALA GLY TYR LYS GLY ARG VAL THR GLY TRP GLY ASN SEQRES 12 H 259 LEU LYS GLU THR TRP THR ALA ASN VAL GLY LYS GLY GLN SEQRES 13 H 259 PRO SER VAL LEU GLN VAL VAL ASN LEU PRO ILE VAL GLU SEQRES 14 H 259 ARG PRO VAL CYS LYS ASP SER THR ARG ILE ARG ILE THR SEQRES 15 H 259 ASP ASN MET PHE CYS ALA GLY TYR LYS PRO ASP GLU GLY SEQRES 16 H 259 LYS ARG GLY ASP ALA CYS GLU GLY ASP SER GLY GLY PRO SEQRES 17 H 259 PHE VAL MET LYS SER PRO PHE ASN ASN ARG TRP TYR GLN SEQRES 18 H 259 MET GLY ILE VAL SER TRP GLY GLU GLY CYS ASP ARG ASP SEQRES 19 H 259 GLY LYS TYR GLY PHE TYR THR HIS VAL PHE ARG LEU LYS SEQRES 20 H 259 LYS TRP ILE GLN LYS VAL ILE ASP GLN PHE GLY GLU SEQRES 1 I 12 GLY ASP PHE GLU GLU ILE PRO GLU GLU TYS LEU GLN MODRES 6GBW TYS I 526 TYR MODIFIED RESIDUE HET TYS I 526 25 HET NAG H 301 14 HET NA H 302 1 HET NA H 303 1 HET DMS H 304 4 HET DMS H 305 8 HET EU5 H 306 39 HETNAM TYS O-SULFO-L-TYROSINE HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM NA SODIUM ION HETNAM DMS DIMETHYL SULFOXIDE HETNAM EU5 (2~{S})-~{N}-[[2-(AMINOMETHYL)-5-CHLORANYL- HETNAM 2 EU5 PHENYL]METHYL]-1-[(2~{S})-5-CARBAMIMIDAMIDO-2- HETNAM 3 EU5 [(PHENYLMETHYL)SULFONYLAMINO]PENTANOYL]PYRROLIDINE-2- HETNAM 4 EU5 CARBOXAMIDE HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE FORMUL 3 TYS C9 H11 N O6 S FORMUL 4 NAG C8 H15 N O6 FORMUL 5 NA 2(NA 1+) FORMUL 7 DMS 2(C2 H6 O S) FORMUL 9 EU5 C26 H36 CL N7 O4 S FORMUL 10 HOH *239(H2 O) HELIX 1 AA1 PHE L 7 SER L 11 5 5 HELIX 2 AA2 THR L 14B TYR L 14J 1 9 HELIX 3 AA3 ALA H 55 CYS H 58 5 4 HELIX 4 AA4 PRO H 60B ASP H 60E 5 4 HELIX 5 AA5 THR H 60I ASN H 62 5 3 HELIX 6 AA6 ASP H 125 LEU H 130 1 9 HELIX 7 AA7 GLU H 164 SER H 171 1 8 HELIX 8 AA8 LYS H 185 GLY H 186C 5 5 HELIX 9 AA9 LEU H 234 PHE H 245 1 12 HELIX 10 AB1 PRO I 523 LEU I 527 5 5 SHEET 1 AA1 7 SER H 20 ASP H 21 0 SHEET 2 AA1 7 GLN H 156 PRO H 161 -1 O VAL H 157 N SER H 20 SHEET 3 AA1 7 LYS H 135 GLY H 140 -1 N VAL H 138 O VAL H 158 SHEET 4 AA1 7 PRO H 198 LYS H 202 -1 O VAL H 200 N ARG H 137 SHEET 5 AA1 7 TRP H 207 TRP H 215 -1 O TYR H 208 N MET H 201 SHEET 6 AA1 7 GLY H 226 HIS H 230 -1 O PHE H 227 N TRP H 215 SHEET 7 AA1 7 MET H 180 ALA H 183 -1 N PHE H 181 O TYR H 228 SHEET 1 AA2 7 LYS H 81 SER H 83 0 SHEET 2 AA2 7 LEU H 64 ILE H 68 -1 N ILE H 68 O LYS H 81 SHEET 3 AA2 7 GLN H 30 ARG H 35 -1 N PHE H 34 O LEU H 65 SHEET 4 AA2 7 GLU H 39 LEU H 46 -1 O LEU H 41 N LEU H 33 SHEET 5 AA2 7 TRP H 51 THR H 54 -1 O LEU H 53 N SER H 45 SHEET 6 AA2 7 ALA H 104 LEU H 108 -1 O ALA H 104 N THR H 54 SHEET 7 AA2 7 LEU H 85 ILE H 90 -1 N GLU H 86 O LYS H 107 SHEET 1 AA3 2 LEU H 60 TYR H 60A 0 SHEET 2 AA3 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 2.03 SSBOND 4 CYS H 191 CYS H 220 1555 1555 2.07 LINK C GLU I 525 N TYS I 526 1555 1555 1.33 LINK C TYS I 526 N LEU I 527 1555 1555 1.33 LINK O LYS H 169 NA NA H 302 1555 1555 2.36 LINK O THR H 172 NA NA H 302 1555 1555 2.33 LINK O PHE H 204A NA NA H 302 1555 4556 2.38 LINK O ARG H 221A NA NA H 303 1555 1555 2.33 LINK O LYS H 224 NA NA H 303 1555 1555 2.41 LINK NA NA H 302 O HOH H 462 1555 1555 2.68 LINK NA NA H 302 O HOH H 507 1555 4546 2.39 LINK NA NA H 302 O HOH H 540 1555 1555 2.43 LINK NA NA H 303 O HOH H 472 1555 1555 2.49 LINK NA NA H 303 O HOH H 490 1555 1555 2.66 LINK NA NA H 303 O HOH H 494 1555 1555 2.37 LINK NA NA H 303 O HOH H 560 1555 1555 2.37 CISPEP 1 SER H 36A PRO H 37 0 -4.62 CRYST1 69.840 71.119 72.858 90.00 100.58 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 0.014318 0.000000 0.002675 0.00000 SCALE2 0.000000 0.014061 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013963 0.00000