HEADER CELL ADHESION 30-MAY-16 5K8R TITLE STRUCTURE OF HUMAN CLUSTERED PROTOCADHERIN GAMMA B3 EC1-4 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTOCADHERIN GAMMA-B3; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 31-444; COMPND 5 SYNONYM: PCDH-GAMMA-B3; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: PCDHGB3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CLUSTERED PROTOCADHERIN, PROTOCADHERIN, CELL ADHESION EXPDTA X-RAY DIFFRACTION AUTHOR J.M.NICOLUDIS,B.E.VOGT,R.GAUDET REVDAT 4 27-SEP-23 5K8R 1 LINK REVDAT 3 25-DEC-19 5K8R 1 REMARK REVDAT 2 13-SEP-17 5K8R 1 REMARK REVDAT 1 24-AUG-16 5K8R 0 JRNL AUTH J.M.NICOLUDIS,B.E.VOGT,A.G.GREEN,C.P.SCHARFE,D.S.MARKS, JRNL AUTH 2 R.GAUDET JRNL TITL ANTIPARALLEL PROTOCADHERIN HOMODIMERS USE DISTINCT AFFINITY- JRNL TITL 2 AND SPECIFICITY-MEDIATING REGIONS IN CADHERIN REPEATS 1-4. JRNL REF ELIFE V. 5 2016 JRNL REFN ESSN 2050-084X JRNL PMID 27472898 JRNL DOI 10.7554/ELIFE.18449 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX DEV_2276 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.35 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.7 REMARK 3 NUMBER OF REFLECTIONS : 18204 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.211 REMARK 3 R VALUE (WORKING SET) : 0.205 REMARK 3 FREE R VALUE : 0.259 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.960 REMARK 3 FREE R VALUE TEST SET COUNT : 1814 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 49.6128 - 5.8755 1.00 1478 164 0.1813 0.2390 REMARK 3 2 5.8755 - 4.6646 1.00 1401 156 0.1666 0.2249 REMARK 3 3 4.6646 - 4.0753 1.00 1389 157 0.1489 0.1987 REMARK 3 4 4.0753 - 3.7028 1.00 1379 154 0.1707 0.2166 REMARK 3 5 3.7028 - 3.4375 1.00 1352 152 0.2003 0.2597 REMARK 3 6 3.4375 - 3.2349 1.00 1358 149 0.2193 0.2599 REMARK 3 7 3.2349 - 3.0729 1.00 1389 152 0.2375 0.3388 REMARK 3 8 3.0729 - 2.9392 1.00 1335 150 0.2715 0.3370 REMARK 3 9 2.9392 - 2.8260 1.00 1359 156 0.2766 0.2989 REMARK 3 10 2.8260 - 2.7285 0.99 1335 153 0.2923 0.3084 REMARK 3 11 2.7285 - 2.6432 0.90 1229 114 0.2922 0.3353 REMARK 3 12 2.6432 - 2.5676 0.64 868 102 0.2898 0.3711 REMARK 3 13 2.5676 - 2.5001 0.38 518 55 0.2604 0.3147 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) : 0.350 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.500 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 37.27 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 : 0.006 3295 REMARK 3 ANGLE : 0.618 4477 REMARK 3 CHIRALITY : 0.052 516 REMARK 3 PLANARITY : 0.005 594 REMARK 3 DIHEDRAL : 14.097 1240 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: NULL REMARK 4 REMARK 4 5K8R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-MAY-16. REMARK 100 THE DEPOSITION ID IS D_1000221901. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-NOV-15 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 : 24-ID-E REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97918 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19844 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 47.350 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.0 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : 0.13340 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.0600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 42.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.70 REMARK 200 R MERGE FOR SHELL (I) : 1.96200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.980 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: 4ZI9 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.58 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES PH 7 4% ETHYLENE GLYCOL 5% REMARK 280 PEG500MME, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 26.82950 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 26.82950 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 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 64.44050 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 80.61450 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 64.44050 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 80.61450 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 26.82950 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 64.44050 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 80.61450 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 26.82950 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 64.44050 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 80.61450 REMARK 290 SMTRY3 8 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5690 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 43260 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -139.0 KCAL/MOL 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 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 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 OD1 ASP A 171 OE1 GLU A 173 2.04 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OD1 ASN A 359 OD1 ASN A 359 3652 1.02 REMARK 500 CG ASN A 359 OD1 ASN A 359 3652 2.18 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 PRO A 32 CD PRO A 32 N 0.087 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 PRO A 2 C - N - CD ANGL. DEV. = 16.4 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 ASP A 30 35.61 -146.10 REMARK 500 ASN A 359 78.41 -118.88 REMARK 500 PRO A 361 37.57 -78.34 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 CA A 502 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 9 OE1 REMARK 620 2 GLU A 10 OE2 93.0 REMARK 620 3 ASP A 61 OD1 87.2 75.8 REMARK 620 4 GLU A 63 OE1 77.8 153.9 79.4 REMARK 620 5 ASP A 98 OD2 108.6 92.4 161.0 113.7 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 503 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 9 OE2 REMARK 620 2 GLU A 63 OE1 83.2 REMARK 620 3 GLU A 63 OE2 99.2 48.8 REMARK 620 4 ASP A 95 OD1 71.1 114.4 76.7 REMARK 620 5 ILE A 96 O 90.0 159.8 151.4 80.9 REMARK 620 6 ASP A 98 OD1 98.6 87.9 130.0 153.2 74.2 REMARK 620 7 ASP A 131 OD1 171.0 95.2 73.3 101.8 94.3 90.2 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 501 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 97 OD1 REMARK 620 2 ASN A 99 O 92.6 REMARK 620 3 ASP A 129 OD1 149.3 88.1 REMARK 620 4 ASP A 129 OD2 158.5 98.2 50.2 REMARK 620 5 ASP A 131 OD2 74.1 78.1 76.0 126.3 REMARK 620 6 ASN A 135 O 83.7 175.7 93.8 86.0 98.6 REMARK 620 7 ASP A 186 OD2 73.6 90.6 137.1 87.7 145.1 90.7 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 508 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 114 OE1 REMARK 620 2 ASP A 171 OD1 91.1 REMARK 620 3 GLU A 173 OE2 70.0 96.8 REMARK 620 4 ASP A 207 OD1 93.6 153.6 60.9 REMARK 620 5 ASP A 207 OD2 74.1 159.4 91.5 44.5 REMARK 620 6 HOH A 663 O 103.3 75.6 170.1 128.0 93.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 509 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 114 OE2 REMARK 620 2 ASP A 204 OD1 71.5 REMARK 620 3 ALA A 205 O 80.9 78.7 REMARK 620 4 ASP A 207 OD1 105.9 162.1 83.5 REMARK 620 5 ASP A 240 OD1 168.7 100.1 90.1 79.6 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 507 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 206 OD1 REMARK 620 2 ASN A 208 O 115.5 REMARK 620 3 ASP A 238 OD1 154.6 77.9 REMARK 620 4 ASP A 238 OD2 141.4 90.9 53.3 REMARK 620 5 ASP A 240 OD2 73.3 84.7 87.3 140.2 REMARK 620 6 ASN A 244 O 80.6 161.8 84.0 79.7 92.5 REMARK 620 7 ASP A 293 OD2 70.7 95.6 131.9 79.6 140.1 98.0 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 505 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 223 OE2 REMARK 620 2 GLU A 280 OE1 95.2 REMARK 620 3 GLU A 280 OE2 128.5 49.4 REMARK 620 4 ASP A 309 OD1 84.4 121.1 86.2 REMARK 620 5 GLU A 310 O 72.6 156.9 152.5 78.1 REMARK 620 6 ASP A 312 OD1 78.2 87.7 125.8 147.7 70.8 REMARK 620 7 ASP A 345 OD1 156.6 95.3 73.3 107.8 90.0 81.3 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 506 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 223 OE1 REMARK 620 2 ASP A 278 OD1 87.4 REMARK 620 3 GLU A 280 OE1 82.8 82.9 REMARK 620 4 ASP A 312 OD1 95.2 171.8 89.7 REMARK 620 5 ASP A 312 OD2 103.1 139.5 136.7 47.3 REMARK 620 6 HOH A 609 O 93.0 59.2 142.1 128.2 81.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 504 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 311 OD1 REMARK 620 2 ASN A 313 O 99.1 REMARK 620 3 ASP A 343 OD1 155.4 86.7 REMARK 620 4 ASP A 343 OD2 153.5 81.4 50.8 REMARK 620 5 ASP A 345 OD2 69.9 78.0 134.6 84.5 REMARK 620 6 ASN A 349 O 91.4 169.5 84.0 88.8 105.1 REMARK 620 7 ASP A 396 OD2 70.6 91.8 85.5 135.9 136.8 92.5 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 512 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 328 O REMARK 620 2 LEU A 380 O 85.9 REMARK 620 3 ASP A 381 OD2 132.0 55.1 REMARK 620 4 GLN A 384 OE1 120.0 34.2 26.6 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 507 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 508 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 509 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 510 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 511 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 512 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EPE A 513 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 514 DBREF 5K8R A 1 414 UNP Q9Y5G1 PCDGF_HUMAN 31 444 SEQRES 1 A 414 GLU PRO ILE ARG TYR ALA ILE PRO GLU GLU LEU ASP ARG SEQRES 2 A 414 GLY SER LEU VAL GLY ASN LEU ALA LYS ASP LEU GLY PHE SEQRES 3 A 414 GLY VAL GLY ASP LEU PRO THR ARG ASN LEU ARG VAL ILE SEQRES 4 A 414 ALA GLU LYS LYS PHE PHE THR VAL SER PRO GLU ASN GLY SEQRES 5 A 414 ASN LEU LEU VAL SER ASP ARG ILE ASP ARG GLU GLU ILE SEQRES 6 A 414 CYS GLY LYS LYS SER THR CYS VAL LEU GLU PHE GLU MET SEQRES 7 A 414 VAL ALA GLU LYS PRO LEU ASN PHE PHE HIS VAL THR VAL SEQRES 8 A 414 LEU ILE GLN ASP ILE ASN ASP ASN PRO PRO THR PHE SER SEQRES 9 A 414 GLN ASN ILE THR GLU LEU GLU ILE SER GLU LEU ALA LEU SEQRES 10 A 414 THR GLY ALA THR PHE ALA LEU GLU SER ALA GLN ASP PRO SEQRES 11 A 414 ASP VAL GLY VAL ASN SER LEU GLN GLN TYR TYR LEU SER SEQRES 12 A 414 PRO ASP PRO HIS PHE SER LEU ILE GLN LYS GLU ASN LEU SEQRES 13 A 414 ASP GLY SER ARG TYR PRO GLU LEU VAL LEU LYS ALA PRO SEQRES 14 A 414 LEU ASP ARG GLU GLU GLN PRO HIS HIS HIS LEU VAL LEU SEQRES 15 A 414 THR ALA VAL ASP GLY GLY GLU PRO SER ARG SER CYS THR SEQRES 16 A 414 THR GLN ILE ARG VAL ILE VAL ALA ASP ALA ASN ASP ASN SEQRES 17 A 414 PRO PRO VAL PHE THR GLN ASP MET TYR ARG VAL ASN VAL SEQRES 18 A 414 ALA GLU ASN LEU PRO ALA GLY SER SER VAL LEU LYS VAL SEQRES 19 A 414 MET ALA ILE ASP MET ASP GLU GLY ILE ASN ALA GLU ILE SEQRES 20 A 414 ILE TYR ALA PHE ILE ASN ILE GLY LYS GLU VAL ARG GLN SEQRES 21 A 414 LEU PHE LYS LEU ASP SER LYS THR GLY GLU LEU THR THR SEQRES 22 A 414 ILE GLY GLU LEU ASP PHE GLU GLU ARG ASP SER TYR THR SEQRES 23 A 414 ILE GLY VAL GLU ALA LYS ASP GLY GLY HIS HIS THR ALA SEQRES 24 A 414 TYR CYS LYS VAL GLN ILE ASP ILE SER ASP GLU ASN ASP SEQRES 25 A 414 ASN ALA PRO GLU ILE THR LEU ALA SER GLU SER GLN HIS SEQRES 26 A 414 ILE GLN GLU ASP ALA GLU LEU GLY THR ALA VAL ALA LEU SEQRES 27 A 414 ILE LYS THR HIS ASP LEU ASP SER GLY PHE ASN GLY GLU SEQRES 28 A 414 ILE LEU CYS GLN LEU LYS GLY ASN PHE PRO PHE LYS ILE SEQRES 29 A 414 VAL GLN ASP THR LYS ASN THR TYR ARG LEU VAL THR ASP SEQRES 30 A 414 GLY ALA LEU ASP ARG GLU GLN ILE PRO GLU TYR ASN VAL SEQRES 31 A 414 THR ILE THR ALA THR ASP LYS GLY ASN PRO PRO LEU SER SEQRES 32 A 414 SER SER LYS THR ILE THR LEU HIS ILE LEU ASP HET CA A 501 1 HET CA A 502 1 HET CA A 503 1 HET CA A 504 1 HET CA A 505 1 HET CA A 506 1 HET CA A 507 1 HET CA A 508 1 HET CA A 509 1 HET CL A 510 1 HET CL A 511 1 HET NA A 512 1 HET EPE A 513 15 HET EDO A 514 4 HETNAM CA CALCIUM ION HETNAM CL CHLORIDE ION HETNAM NA SODIUM ION HETNAM EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HETNAM EDO 1,2-ETHANEDIOL HETSYN EPE HEPES HETSYN EDO ETHYLENE GLYCOL FORMUL 2 CA 9(CA 2+) FORMUL 11 CL 2(CL 1-) FORMUL 13 NA NA 1+ FORMUL 14 EPE C8 H18 N2 O4 S FORMUL 15 EDO C2 H6 O2 FORMUL 16 HOH *120(H2 O) HELIX 1 AA1 LEU A 20 LEU A 24 1 5 HELIX 2 AA2 GLY A 27 GLY A 29 5 3 HELIX 3 AA3 ASP A 30 ASN A 35 1 6 HELIX 4 AA4 ASP A 61 CYS A 66 1 6 HELIX 5 AA5 VAL A 132 SER A 136 5 5 HELIX 6 AA6 GLU A 241 ALA A 245 5 5 HELIX 7 AA7 GLY A 255 GLN A 260 1 6 HELIX 8 AA8 SER A 346 GLY A 350 5 5 SHEET 1 AA1 4 ILE A 3 PRO A 8 0 SHEET 2 AA1 4 ASN A 85 GLN A 94 1 O LEU A 92 N TYR A 5 SHEET 3 AA1 4 VAL A 73 ALA A 80 -1 N PHE A 76 O VAL A 89 SHEET 4 AA1 4 ARG A 37 ILE A 39 -1 N ARG A 37 O VAL A 79 SHEET 1 AA2 3 LEU A 16 ASN A 19 0 SHEET 2 AA2 3 ASN A 53 VAL A 56 -1 O LEU A 54 N VAL A 17 SHEET 3 AA2 3 PHE A 45 VAL A 47 -1 N THR A 46 O LEU A 55 SHEET 1 AA3 4 ILE A 107 SER A 113 0 SHEET 2 AA3 4 SER A 193 ALA A 203 1 O GLN A 197 N THR A 108 SHEET 3 AA3 4 HIS A 177 ASP A 186 -1 N LEU A 180 O ILE A 198 SHEET 4 AA3 4 GLN A 138 LEU A 142 -1 N TYR A 141 O THR A 183 SHEET 1 AA4 3 THR A 121 ALA A 123 0 SHEET 2 AA4 3 ARG A 160 LEU A 166 -1 O LEU A 164 N PHE A 122 SHEET 3 AA4 3 PHE A 148 GLU A 154 -1 N SER A 149 O VAL A 165 SHEET 1 AA5 2 VAL A 211 PHE A 212 0 SHEET 2 AA5 2 ALA A 236 ILE A 237 -1 O ILE A 237 N VAL A 211 SHEET 1 AA6 4 MET A 216 ALA A 222 0 SHEET 2 AA6 4 THR A 298 SER A 308 1 O ASP A 306 N VAL A 219 SHEET 3 AA6 4 SER A 284 LYS A 292 -1 N VAL A 289 O CYS A 301 SHEET 4 AA6 4 ILE A 248 ILE A 252 -1 N ALA A 250 O GLU A 290 SHEET 1 AA7 3 SER A 230 LYS A 233 0 SHEET 2 AA7 3 GLU A 270 THR A 273 -1 O LEU A 271 N VAL A 231 SHEET 3 AA7 3 PHE A 262 LEU A 264 -1 N LYS A 263 O THR A 272 SHEET 1 AA8 4 GLU A 316 SER A 321 0 SHEET 2 AA8 4 ALA A 335 HIS A 342 -1 O HIS A 342 N GLU A 316 SHEET 3 AA8 4 THR A 371 THR A 376 -1 O LEU A 374 N VAL A 336 SHEET 4 AA8 4 PHE A 362 GLN A 366 -1 N LYS A 363 O VAL A 375 SHEET 1 AA9 4 HIS A 325 GLN A 327 0 SHEET 2 AA9 4 SER A 403 LEU A 413 1 O LEU A 413 N ILE A 326 SHEET 3 AA9 4 GLU A 387 ASP A 396 -1 N ILE A 392 O LYS A 406 SHEET 4 AA9 4 ILE A 352 LYS A 357 -1 N GLN A 355 O THR A 393 SSBOND 1 CYS A 66 CYS A 72 1555 1555 2.03 LINK OE1 GLU A 9 CA CA A 502 1555 1555 2.71 LINK OE2 GLU A 9 CA CA A 503 1555 1555 2.49 LINK OE2 GLU A 10 CA CA A 502 1555 1555 2.63 LINK OD1 ASP A 61 CA CA A 502 1555 1555 2.42 LINK OE1 GLU A 63 CA CA A 502 1555 1555 2.44 LINK OE1 GLU A 63 CA CA A 503 1555 1555 2.83 LINK OE2 GLU A 63 CA CA A 503 1555 1555 2.40 LINK OD1 ASP A 95 CA CA A 503 1555 1555 2.41 LINK O ILE A 96 CA CA A 503 1555 1555 2.40 LINK OD1 ASN A 97 CA CA A 501 1555 1555 2.43 LINK OD2 ASP A 98 CA CA A 502 1555 1555 2.44 LINK OD1 ASP A 98 CA CA A 503 1555 1555 2.46 LINK O ASN A 99 CA CA A 501 1555 1555 2.38 LINK OE1 GLU A 114 CA CA A 508 1555 1555 2.55 LINK OE2 GLU A 114 CA CA A 509 1555 1555 2.42 LINK OD1 ASP A 129 CA CA A 501 1555 1555 2.73 LINK OD2 ASP A 129 CA CA A 501 1555 1555 2.39 LINK OD2 ASP A 131 CA CA A 501 1555 1555 2.51 LINK OD1 ASP A 131 CA CA A 503 1555 1555 2.46 LINK O ASN A 135 CA CA A 501 1555 1555 2.40 LINK OD1 ASP A 171 CA CA A 508 1555 1555 2.35 LINK OE2 GLU A 173 CA CA A 508 1555 1555 3.17 LINK OD2 ASP A 186 CA CA A 501 1555 1555 2.74 LINK OD1 ASP A 204 CA CA A 509 1555 1555 2.59 LINK O ALA A 205 CA CA A 509 1555 1555 2.44 LINK OD1 ASN A 206 CA CA A 507 1555 1555 2.41 LINK OD1 ASP A 207 CA CA A 508 1555 1555 3.10 LINK OD2 ASP A 207 CA CA A 508 1555 1555 2.51 LINK OD1 ASP A 207 CA CA A 509 1555 1555 2.49 LINK O ASN A 208 CA CA A 507 1555 1555 2.37 LINK OE2 GLU A 223 CA CA A 505 1555 1555 2.46 LINK OE1 GLU A 223 CA CA A 506 1555 1555 2.46 LINK OD1 ASP A 238 CA CA A 507 1555 1555 2.48 LINK OD2 ASP A 238 CA CA A 507 1555 1555 2.41 LINK OD2 ASP A 240 CA CA A 507 1555 1555 2.78 LINK OD1 ASP A 240 CA CA A 509 1555 1555 2.77 LINK O ASN A 244 CA CA A 507 1555 1555 2.39 LINK OD1 ASP A 278 CA CA A 506 1555 1555 2.51 LINK OE1 GLU A 280 CA CA A 505 1555 1555 2.74 LINK OE2 GLU A 280 CA CA A 505 1555 1555 2.50 LINK OE1 GLU A 280 CA CA A 506 1555 1555 2.43 LINK OD2 ASP A 293 CA CA A 507 1555 1555 2.70 LINK OD1 ASP A 309 CA CA A 505 1555 1555 2.48 LINK O GLU A 310 CA CA A 505 1555 1555 2.44 LINK OD1 ASN A 311 CA CA A 504 1555 1555 2.46 LINK OD1 ASP A 312 CA CA A 505 1555 1555 2.73 LINK OD1 ASP A 312 CA CA A 506 1555 1555 2.92 LINK OD2 ASP A 312 CA CA A 506 1555 1555 2.44 LINK O ASN A 313 CA CA A 504 1555 1555 2.43 LINK O GLU A 328 NA NA A 512 1555 1555 2.46 LINK OD1 ASP A 343 CA CA A 504 1555 1555 2.46 LINK OD2 ASP A 343 CA CA A 504 1555 1555 2.64 LINK OD2 ASP A 345 CA CA A 504 1555 1555 2.55 LINK OD1 ASP A 345 CA CA A 505 1555 1555 2.53 LINK O ASN A 349 CA CA A 504 1555 1555 2.48 LINK O LEU A 380 NA NA A 512 1555 1555 2.48 LINK OD2 ASP A 381 NA NA A 512 1555 3652 2.42 LINK OE1 GLN A 384 NA NA A 512 1555 3652 3.18 LINK OD2 ASP A 396 CA CA A 504 1555 1555 2.71 LINK CA CA A 506 O HOH A 609 1555 1555 2.52 LINK CA CA A 508 O HOH A 663 1555 1555 2.50 CISPEP 1 GLU A 1 PRO A 2 0 0.02 CISPEP 2 LYS A 82 PRO A 83 0 -4.15 CISPEP 3 GLU A 189 PRO A 190 0 -0.76 CISPEP 4 ASN A 399 PRO A 400 0 -0.29 SITE 1 AC1 6 ASN A 97 ASN A 99 ASP A 129 ASP A 131 SITE 2 AC1 6 ASN A 135 ASP A 186 SITE 1 AC2 5 GLU A 9 GLU A 10 ASP A 61 GLU A 63 SITE 2 AC2 5 ASP A 98 SITE 1 AC3 6 GLU A 9 GLU A 63 ASP A 95 ILE A 96 SITE 2 AC3 6 ASP A 98 ASP A 131 SITE 1 AC4 6 ASN A 311 ASN A 313 ASP A 343 ASP A 345 SITE 2 AC4 6 ASN A 349 ASP A 396 SITE 1 AC5 7 GLU A 223 GLU A 280 ASP A 309 GLU A 310 SITE 2 AC5 7 ASP A 312 ASP A 345 CA A 506 SITE 1 AC6 7 GLU A 223 ASP A 278 GLU A 280 ASP A 312 SITE 2 AC6 7 ASN A 313 CA A 505 HOH A 609 SITE 1 AC7 6 ASN A 206 ASN A 208 ASP A 238 ASP A 240 SITE 2 AC7 6 ASN A 244 ASP A 293 SITE 1 AC8 5 GLU A 114 ASP A 171 GLU A 173 ASP A 207 SITE 2 AC8 5 HOH A 663 SITE 1 AC9 7 GLU A 114 GLU A 173 ASP A 204 ALA A 205 SITE 2 AC9 7 ASP A 207 ASN A 208 ASP A 240 SITE 1 AD1 2 ARG A 34 ASN A 85 SITE 1 AD2 1 VAL A 258 SITE 1 AD3 3 GLU A 328 ASP A 329 LEU A 380 SITE 1 AD4 8 SER A 126 ASN A 155 TYR A 161 GLU A 163 SITE 2 AD4 8 ILE A 252 ASN A 253 HOH A 614 HOH A 624 SITE 1 AD5 1 HOH A 645 CRYST1 128.881 161.229 53.659 90.00 90.00 90.00 C 2 2 21 8 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 0.007759 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006202 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018636 0.00000