HEADER HORMONE 01-JUL-11 3SP8 TITLE CRYSTAL STRUCTURE OF NK2 IN COMPLEX WITH FRACTIONATED HEPARIN DP10 COMPND MOL_ID: 1; COMPND 2 MOLECULE: HEPATOCYTE GROWTH FACTOR ALPHA CHAIN; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: NK2; COMPND 5 SYNONYM: HEPATOPOEITIN-A, SCATTER FACTOR, SF; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: HGF, HPTA; SOURCE 6 EXPRESSION_SYSTEM: PICHIA PASTORIS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 4922 KEYWDS KRINGLE DOMAIN, MET TYROSINE KINASE, HORMONE EXPDTA X-RAY DIFFRACTION AUTHOR R.RECACHA,B.MULLOY,E.GHERARDI REVDAT 3 27-NOV-24 3SP8 1 REMARK REVDAT 2 13-SEP-23 3SP8 1 REMARK SEQADV REVDAT 1 04-JUL-12 3SP8 0 JRNL AUTH R.RECACHA,B.MULLOY,E.GHERARDI JRNL TITL CRYSTAL STRUCTURE OF NK2 IN COMPLEX WITH FRACTIONATED JRNL TITL 2 HEPARIN DP10 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH D.LIETHA,D.Y.CHIRGADZE,T.L BLUNDELL,E.GHERARDI,B.MULLOY REMARK 1 TITL CRYSTAL STRUCTURES OF NK1 HEPARIN COMPLEXES REVEAL THE BASIS REMARK 1 TITL 2 FOR NK1 ACTIVITY AND ENABLE ENGINEERING OF POTENT AGONISTS REMARK 1 TITL 3 OF THE MET RECEPTOR REMARK 1 REF EMBO J. V. 20 5543 2001 REMARK 1 REFN ISSN 0261-4189 REMARK 1 REFERENCE 2 REMARK 1 AUTH W.D.TOLBERT,J.DAUGHERTY-HOLTROP,G.VANDE WOUDE,H.E.XU, REMARK 1 AUTH 2 E.GHERARDI REMARK 1 TITL STRUCTURAL BASIS FOR AGONISM AND ANTAGONISM OF HEPATOCYTE REMARK 1 TITL 2 GROWTH FACTOR REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 107 13264 2010 REMARK 1 REFN ISSN 0027-8424 REMARK 1 REFERENCE 3 REMARK 1 AUTH K.TAN,M.DUQUETTE,J.H.LIU,K.SHANMUGASUNDARAM,A.JOACHIMIAK, REMARK 1 AUTH 2 J.T.GALLAGHER,A.C.RIGBY,J.H.WANG,J.LAWLER REMARK 1 TITL HEPARIN-INDUCED CIS- AND TRANS-DIMERIZATION MODES OF THE REMARK 1 TITL 2 THROMBOSPONDIN-1 N-TERMINAL DOMAIN REMARK 1 REF J.BIOL.CHEM. V. 283 3932 2008 REMARK 1 REFN ISSN 0021-9258 REMARK 2 REMARK 2 RESOLUTION. 1.86 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.1_743) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.86 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 65.80 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 54379 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.188 REMARK 3 R VALUE (WORKING SET) : 0.187 REMARK 3 FREE R VALUE : 0.217 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.080 REMARK 3 FREE R VALUE TEST SET COUNT : 2763 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 65.8417 - 5.0482 0.99 2574 135 0.1949 0.2118 REMARK 3 2 5.0482 - 4.0071 1.00 2612 121 0.1476 0.1702 REMARK 3 3 4.0071 - 3.5006 1.00 2600 133 0.1606 0.1936 REMARK 3 4 3.5006 - 3.1805 1.00 2567 146 0.1822 0.1936 REMARK 3 5 3.1805 - 2.9526 1.00 2562 164 0.1836 0.2051 REMARK 3 6 2.9526 - 2.7785 1.00 2616 127 0.1887 0.1990 REMARK 3 7 2.7785 - 2.6393 1.00 2576 129 0.1943 0.2391 REMARK 3 8 2.6393 - 2.5244 1.00 2578 134 0.1938 0.2476 REMARK 3 9 2.5244 - 2.4272 1.00 2613 133 0.1993 0.2229 REMARK 3 10 2.4272 - 2.3435 1.00 2577 136 0.1981 0.2521 REMARK 3 11 2.3435 - 2.2702 1.00 2592 133 0.2035 0.2394 REMARK 3 12 2.2702 - 2.2053 1.00 2569 143 0.1964 0.2414 REMARK 3 13 2.2053 - 2.1473 1.00 2586 121 0.1960 0.2076 REMARK 3 14 2.1473 - 2.0949 1.00 2570 129 0.2065 0.2536 REMARK 3 15 2.0949 - 2.0472 1.00 2602 126 0.2127 0.2947 REMARK 3 16 2.0472 - 2.0037 1.00 2559 144 0.2262 0.2854 REMARK 3 17 2.0037 - 1.9636 1.00 2581 154 0.2579 0.3043 REMARK 3 18 1.9636 - 1.9265 1.00 2560 143 0.2558 0.2962 REMARK 3 19 1.9265 - 1.8921 1.00 2552 149 0.2897 0.3025 REMARK 3 20 1.8921 - 1.8600 1.00 2570 163 0.3180 0.3697 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.83 REMARK 3 K_SOL : 0.33 REMARK 3 B_SOL : 45.50 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.570 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.220 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) : -1.01520 REMARK 3 B22 (A**2) : -1.01520 REMARK 3 B33 (A**2) : 2.03030 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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 : 0.004 4630 REMARK 3 ANGLE : 0.883 6270 REMARK 3 CHIRALITY : 0.062 608 REMARK 3 PLANARITY : 0.004 805 REMARK 3 DIHEDRAL : 16.379 1808 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -29.1929 26.8444 -16.1371 REMARK 3 T TENSOR REMARK 3 T11: 0.3089 T22: 0.2744 REMARK 3 T33: 0.2348 T12: 0.0272 REMARK 3 T13: 0.0040 T23: -0.0178 REMARK 3 L TENSOR REMARK 3 L11: 0.5482 L22: 0.9968 REMARK 3 L33: 0.4659 L12: -0.3342 REMARK 3 L13: 0.2864 L23: -0.5337 REMARK 3 S TENSOR REMARK 3 S11: -0.1157 S12: -0.1456 S13: 0.0438 REMARK 3 S21: -0.1346 S22: 0.0488 S23: -0.0685 REMARK 3 S31: 0.0462 S32: -0.1067 S33: 0.0596 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3SP8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-JUL-11. REMARK 100 THE DEPOSITION ID IS D_1000066481. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-JAN-11 REMARK 200 TEMPERATURE (KELVIN) : 172 REMARK 200 PH : 6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97 REMARK 200 MONOCHROMATOR : SI REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 54379 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.860 REMARK 200 RESOLUTION RANGE LOW (A) : 65.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.86 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL 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: 3NH4 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.29 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.69 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50MM MES PH=6.0, 30% MPD, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 21K, TEMPERATURE 294K, PH 6 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 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 66.54000 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 133.08000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 99.81000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 166.35000 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 33.27000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 GLY A 26 REMARK 465 SER A 27 REMARK 465 TYR A 28 REMARK 465 ALA A 29 REMARK 465 GLU A 30 REMARK 465 GLY A 31 REMARK 465 GLN A 32 REMARK 465 ARG A 33 REMARK 465 LYS A 34 REMARK 465 GLY B 26 REMARK 465 SER B 27 REMARK 465 TYR B 28 REMARK 465 ALA B 29 REMARK 465 GLU B 30 REMARK 465 GLY B 31 REMARK 465 GLN B 32 REMARK 465 ARG B 33 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 A 284 CG CD CE NZ REMARK 470 LYS A 289 CG CD CE NZ REMARK 470 LYS B 34 CG CD CE NZ REMARK 470 ARG B 35 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 284 CG CD CE NZ REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LYS A 60 CE NZ REMARK 480 LYS A 62 CE NZ 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 290 O HOH B 336 1.84 REMARK 500 OD1 ASP B 252 O HOH B 292 1.88 REMARK 500 O HOH A 420 O HOH B 399 1.92 REMARK 500 O HOH B 320 O HOH B 326 1.96 REMARK 500 NH1 ARG B 126 O HOH B 412 1.98 REMARK 500 O HOH B 305 O HOH B 307 2.00 REMARK 500 O HOH A 351 O HOH A 455 2.04 REMARK 500 O HOH A 377 O HOH A 400 2.05 REMARK 500 O2 MRD A 1207 O HOH A 330 2.08 REMARK 500 O1S MES B 1202 O HOH B 410 2.10 REMARK 500 O2 MRD A 1203 O HOH A 371 2.13 REMARK 500 O3S MES B 1202 O HOH B 410 2.13 REMARK 500 NE2 HIS A 40 O HOH A 379 2.16 REMARK 500 O3S MES A 1202 O HOH A 321 2.16 REMARK 500 O HOH A 443 O HOH B 333 2.18 REMARK 500 O HOH A 296 O HOH A 301 2.19 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 ASN A 37 88.92 30.17 REMARK 500 SER A 141 29.84 -142.46 REMARK 500 PHE A 162 59.35 -93.31 REMARK 500 GLU A 174 -135.29 46.98 REMARK 500 ASP A 202 77.50 -110.89 REMARK 500 ASP A 202 74.78 -110.89 REMARK 500 SER A 214 -120.45 40.90 REMARK 500 ASP A 257 -129.35 44.16 REMARK 500 ARG B 36 -109.83 -140.99 REMARK 500 ASN B 37 82.59 83.93 REMARK 500 PHE B 162 59.89 -93.10 REMARK 500 GLU B 174 -135.39 48.00 REMARK 500 ASP B 202 75.72 -109.62 REMARK 500 SER B 214 -119.21 45.31 REMARK 500 ASP B 257 -130.76 44.78 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 ASN B 77 LYS B 78 -144.53 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MRD A 1203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MES A 1202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MES A 1201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MRD A 1207 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MRD A 290 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 1209 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 2 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 3 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 5 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 6 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MRD B 1209 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MES B 1202 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MES B 1201 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 7 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 8 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 9 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 10 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3HN4 RELATED DB: PDB REMARK 900 NK2 STRUCTURE REMARK 900 RELATED ID: 3MKP RELATED DB: PDB REMARK 900 NK1 IN COMPLEX WITH HEPARIN REMARK 900 RELATED ID: 1GMN RELATED DB: PDB REMARK 900 NK1 IN COMPLEX WITH HEPARIN REMARK 900 RELATED ID: 1GP9 RELATED DB: PDB REMARK 900 NK1 REMARK 900 RELATED ID: 2OUH RELATED DB: PDB REMARK 900 THROMBOSPONDIN-1 N-TERMINAL DOMAIN IN COMPLEX WITH FRACTIONATED REMARK 900 HEPARIN DP10 DBREF 3SP8 A 28 288 UNP P14210 HGF_HUMAN 28 288 DBREF 3SP8 B 28 288 UNP P14210 HGF_HUMAN 28 288 SEQADV 3SP8 GLY A 26 UNP P14210 EXPRESSION TAG SEQADV 3SP8 SER A 27 UNP P14210 EXPRESSION TAG SEQADV 3SP8 ASP A 146 UNP P14210 GLY 146 ENGINEERED MUTATION SEQADV 3SP8 SER A 214 UNP P14210 CYS 214 ENGINEERED MUTATION SEQADV 3SP8 LYS A 284 UNP P14210 ALA 284 CONFLICT SEQADV 3SP8 LYS A 289 UNP P14210 EXPRESSION TAG SEQADV 3SP8 GLY B 26 UNP P14210 EXPRESSION TAG SEQADV 3SP8 SER B 27 UNP P14210 EXPRESSION TAG SEQADV 3SP8 ASP B 146 UNP P14210 GLY 146 ENGINEERED MUTATION SEQADV 3SP8 SER B 214 UNP P14210 CYS 214 ENGINEERED MUTATION SEQADV 3SP8 LYS B 284 UNP P14210 ALA 284 CONFLICT SEQADV 3SP8 LYS B 289 UNP P14210 EXPRESSION TAG SEQRES 1 A 264 GLY SER TYR ALA GLU GLY GLN ARG LYS ARG ARG ASN THR SEQRES 2 A 264 ILE HIS GLU PHE LYS LYS SER ALA LYS THR THR LEU ILE SEQRES 3 A 264 LYS ILE ASP PRO ALA LEU LYS ILE LYS THR LYS LYS VAL SEQRES 4 A 264 ASN THR ALA ASP GLN CYS ALA ASN ARG CYS THR ARG ASN SEQRES 5 A 264 LYS GLY LEU PRO PHE THR CYS LYS ALA PHE VAL PHE ASP SEQRES 6 A 264 LYS ALA ARG LYS GLN CYS LEU TRP PHE PRO PHE ASN SER SEQRES 7 A 264 MET SER SER GLY VAL LYS LYS GLU PHE GLY HIS GLU PHE SEQRES 8 A 264 ASP LEU TYR GLU ASN LYS ASP TYR ILE ARG ASN CYS ILE SEQRES 9 A 264 ILE GLY LYS GLY ARG SER TYR LYS GLY THR VAL SER ILE SEQRES 10 A 264 THR LYS SER ASP ILE LYS CYS GLN PRO TRP SER SER MET SEQRES 11 A 264 ILE PRO HIS GLU HIS SER PHE LEU PRO SER SER TYR ARG SEQRES 12 A 264 GLY LYS ASP LEU GLN GLU ASN TYR CYS ARG ASN PRO ARG SEQRES 13 A 264 GLY GLU GLU GLY GLY PRO TRP CYS PHE THR SER ASN PRO SEQRES 14 A 264 GLU VAL ARG TYR GLU VAL CYS ASP ILE PRO GLN CYS SER SEQRES 15 A 264 GLU VAL GLU CYS MET THR SER ASN GLY GLU SER TYR ARG SEQRES 16 A 264 GLY LEU MET ASP HIS THR GLU SER GLY LYS ILE CYS GLN SEQRES 17 A 264 ARG TRP ASP HIS GLN THR PRO HIS ARG HIS LYS PHE LEU SEQRES 18 A 264 PRO GLU ARG TYR PRO ASP LYS GLY PHE ASP ASP ASN TYR SEQRES 19 A 264 CYS ARG ASN PRO ASP GLY GLN PRO ARG PRO TRP CYS TYR SEQRES 20 A 264 THR LEU ASP PRO HIS THR ARG TRP GLU TYR CYS LYS ILE SEQRES 21 A 264 LYS THR CYS LYS SEQRES 1 B 264 GLY SER TYR ALA GLU GLY GLN ARG LYS ARG ARG ASN THR SEQRES 2 B 264 ILE HIS GLU PHE LYS LYS SER ALA LYS THR THR LEU ILE SEQRES 3 B 264 LYS ILE ASP PRO ALA LEU LYS ILE LYS THR LYS LYS VAL SEQRES 4 B 264 ASN THR ALA ASP GLN CYS ALA ASN ARG CYS THR ARG ASN SEQRES 5 B 264 LYS GLY LEU PRO PHE THR CYS LYS ALA PHE VAL PHE ASP SEQRES 6 B 264 LYS ALA ARG LYS GLN CYS LEU TRP PHE PRO PHE ASN SER SEQRES 7 B 264 MET SER SER GLY VAL LYS LYS GLU PHE GLY HIS GLU PHE SEQRES 8 B 264 ASP LEU TYR GLU ASN LYS ASP TYR ILE ARG ASN CYS ILE SEQRES 9 B 264 ILE GLY LYS GLY ARG SER TYR LYS GLY THR VAL SER ILE SEQRES 10 B 264 THR LYS SER ASP ILE LYS CYS GLN PRO TRP SER SER MET SEQRES 11 B 264 ILE PRO HIS GLU HIS SER PHE LEU PRO SER SER TYR ARG SEQRES 12 B 264 GLY LYS ASP LEU GLN GLU ASN TYR CYS ARG ASN PRO ARG SEQRES 13 B 264 GLY GLU GLU GLY GLY PRO TRP CYS PHE THR SER ASN PRO SEQRES 14 B 264 GLU VAL ARG TYR GLU VAL CYS ASP ILE PRO GLN CYS SER SEQRES 15 B 264 GLU VAL GLU CYS MET THR SER ASN GLY GLU SER TYR ARG SEQRES 16 B 264 GLY LEU MET ASP HIS THR GLU SER GLY LYS ILE CYS GLN SEQRES 17 B 264 ARG TRP ASP HIS GLN THR PRO HIS ARG HIS LYS PHE LEU SEQRES 18 B 264 PRO GLU ARG TYR PRO ASP LYS GLY PHE ASP ASP ASN TYR SEQRES 19 B 264 CYS ARG ASN PRO ASP GLY GLN PRO ARG PRO TRP CYS TYR SEQRES 20 B 264 THR LEU ASP PRO HIS THR ARG TRP GLU TYR CYS LYS ILE SEQRES 21 B 264 LYS THR CYS LYS HET MRD A1203 8 HET MES A1202 12 HET MES A1201 12 HET MRD A1207 8 HET MRD A 290 8 HET MPD A1209 8 HET SO4 A 1 5 HET SO4 A 2 5 HET SO4 A 3 5 HET SO4 A 4 5 HET SO4 A 5 5 HET SO4 A 6 5 HET MRD B1209 8 HET MES B1202 12 HET MES B1201 12 HET SO4 B 7 5 HET SO4 B 8 5 HET SO4 B 9 5 HET SO4 B 10 5 HETNAM MRD (4R)-2-METHYLPENTANE-2,4-DIOL HETNAM MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL HETNAM SO4 SULFATE ION FORMUL 3 MRD 4(C6 H14 O2) FORMUL 4 MES 4(C6 H13 N O4 S) FORMUL 8 MPD C6 H14 O2 FORMUL 9 SO4 10(O4 S 2-) FORMUL 22 HOH *359(H2 O) HELIX 1 1 THR A 38 HIS A 40 5 3 HELIX 2 2 THR A 66 ARG A 76 1 11 HELIX 3 3 LYS A 122 ARG A 126 1 5 HELIX 4 4 GLN A 205 GLU A 210 1 6 HELIX 5 5 THR B 38 HIS B 40 5 3 HELIX 6 6 THR B 66 ARG B 76 1 11 HELIX 7 7 LYS B 122 ARG B 126 1 5 HELIX 8 8 LEU B 163 TYR B 167 5 5 HELIX 9 9 GLN B 205 GLU B 210 1 6 HELIX 10 10 LEU B 246 TYR B 250 5 5 SHEET 1 A 5 PHE A 42 SER A 45 0 SHEET 2 A 5 PHE A 116 ASN A 121 -1 O GLU A 120 N LYS A 43 SHEET 3 A 5 ALA A 86 ASP A 90 -1 N PHE A 87 O TYR A 119 SHEET 4 A 5 GLN A 95 PHE A 99 -1 O PHE A 99 N ALA A 86 SHEET 5 A 5 LYS A 60 LYS A 63 -1 N LYS A 60 O TRP A 98 SHEET 1 B 2 THR A 48 LYS A 52 0 SHEET 2 B 2 VAL A 108 PHE A 112 -1 O LYS A 109 N ILE A 51 SHEET 1 C 2 TRP A 188 PHE A 190 0 SHEET 2 C 2 TYR A 198 VAL A 200 -1 O GLU A 199 N CYS A 189 SHEET 1 D 2 CYS A 211 MET A 212 0 SHEET 2 D 2 LYS A 286 THR A 287 1 O LYS A 286 N MET A 212 SHEET 1 E 2 TRP A 270 TYR A 272 0 SHEET 2 E 2 TRP A 280 TYR A 282 -1 O GLU A 281 N CYS A 271 SHEET 1 F 5 PHE B 42 SER B 45 0 SHEET 2 F 5 PHE B 116 ASN B 121 -1 O GLU B 120 N LYS B 43 SHEET 3 F 5 ALA B 86 ASP B 90 -1 N PHE B 87 O TYR B 119 SHEET 4 F 5 GLN B 95 PHE B 99 -1 O PHE B 99 N ALA B 86 SHEET 5 F 5 LYS B 60 LYS B 63 -1 N LYS B 60 O TRP B 98 SHEET 1 G 2 THR B 48 LYS B 52 0 SHEET 2 G 2 VAL B 108 PHE B 112 -1 O LYS B 109 N ILE B 51 SHEET 1 H 2 TRP B 188 PHE B 190 0 SHEET 2 H 2 TYR B 198 VAL B 200 -1 O GLU B 199 N CYS B 189 SHEET 1 I 2 CYS B 211 MET B 212 0 SHEET 2 I 2 LYS B 286 THR B 287 1 O LYS B 286 N MET B 212 SHEET 1 J 2 TRP B 270 TYR B 272 0 SHEET 2 J 2 TRP B 280 TYR B 282 -1 O GLU B 281 N CYS B 271 SSBOND 1 CYS A 70 CYS A 96 1555 1555 2.03 SSBOND 2 CYS A 74 CYS A 84 1555 1555 2.07 SSBOND 3 CYS A 128 CYS A 206 1555 1555 2.03 SSBOND 4 CYS A 149 CYS A 189 1555 1555 2.04 SSBOND 5 CYS A 177 CYS A 201 1555 1555 2.03 SSBOND 6 CYS A 211 CYS A 288 1555 1555 2.04 SSBOND 7 CYS A 232 CYS A 271 1555 1555 2.03 SSBOND 8 CYS A 260 CYS A 283 1555 1555 2.04 SSBOND 9 CYS B 70 CYS B 96 1555 1555 2.03 SSBOND 10 CYS B 74 CYS B 84 1555 1555 2.07 SSBOND 11 CYS B 128 CYS B 206 1555 1555 2.02 SSBOND 12 CYS B 149 CYS B 189 1555 1555 2.04 SSBOND 13 CYS B 177 CYS B 201 1555 1555 2.03 SSBOND 14 CYS B 211 CYS B 288 1555 1555 2.04 SSBOND 15 CYS B 232 CYS B 271 1555 1555 2.03 SSBOND 16 CYS B 260 CYS B 283 1555 1555 2.03 CISPEP 1 ILE A 156 PRO A 157 0 2.11 CISPEP 2 THR A 239 PRO A 240 0 2.33 CISPEP 3 ILE B 156 PRO B 157 0 2.30 CISPEP 4 THR B 239 PRO B 240 0 1.24 SITE 1 AC1 2 ARG A 220 HOH A 371 SITE 1 AC2 7 ASP A 264 GLN A 266 TRP A 270 TYR A 272 SITE 2 AC2 7 ARG A 279 TRP A 280 HOH A 321 SITE 1 AC3 9 GLU A 183 TRP A 188 PHE A 190 ARG A 197 SITE 2 AC3 9 TYR A 198 HOH A 387 HOH A 388 SER B 161 SITE 3 AC3 9 HOH B 345 SITE 1 AC4 7 THR A 48 GLU A 111 PHE A 112 HOH A 330 SITE 2 AC4 7 THR B 48 GLU B 111 PHE B 112 SITE 1 AC5 1 PHE A 112 SITE 1 AC6 4 THR A 49 LEU A 50 LEU A 97 GLU A 227 SITE 1 AC7 5 LYS A 62 VAL A 64 ARG A 73 ARG A 76 SITE 2 AC7 5 TRP A 98 SITE 1 AC8 2 LYS A 62 LYS A 63 SITE 1 AC9 2 LYS A 62 ARG A 73 SITE 1 BC1 1 ARG A 134 SITE 1 BC2 3 ARG A 134 SER A 135 HOH A 291 SITE 1 BC3 5 THR B 49 LEU B 50 LEU B 97 PHE B 116 SITE 2 BC3 5 HOH B 402 SITE 1 BC4 8 ASP B 264 GLN B 266 TRP B 270 TYR B 272 SITE 2 BC4 8 ARG B 279 TRP B 280 HOH B 410 HOH B 448 SITE 1 BC5 9 SER A 161 HOH A 388 GLU B 183 TRP B 188 SITE 2 BC5 9 PHE B 190 ARG B 197 TYR B 198 HOH B 298 SITE 3 BC5 9 HOH B 345 SITE 1 BC6 3 VAL B 64 ARG B 73 TRP B 98 SITE 1 BC7 3 LYS B 230 ILE B 231 HOH B 452 SITE 1 BC8 2 GLN B 69 ASN B 72 SITE 1 BC9 4 ILE B 130 LYS B 132 GLY B 133 ARG B 134 CRYST1 75.980 75.980 199.620 90.00 90.00 120.00 P 61 12 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 0.013161 0.007599 0.000000 0.00000 SCALE2 0.000000 0.015197 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005010 0.00000