HEADER CELL ADHESION 06-JAN-20 6VFP TITLE CRYSTAL STRUCTURE OF HUMAN PROTOCADHERIN 1 EC1-EC4 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTOCADHERIN-1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CADHERIN-LIKE PROTEIN 1,PROTOCADHERIN-42,PC42; COMPND 5 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: PCDH1; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: HEK293 KEYWDS CADHERIN EXTRACELLULAR REGION, NON-CLUSTERED DELTA1 FAMILY KEYWDS 2 PROTOCADHERIN, HOMOPHILIC ADHESION/RECOGNITION CALCIUM-DEPENDENT KEYWDS 3 ADHESION MOLECULE, CELL ADHESION EXPDTA X-RAY DIFFRACTION AUTHOR J.BRASCH,O.J.HARRISON,L.SHAPIRO REVDAT 3 11-OCT-23 6VFP 1 HETSYN REVDAT 2 29-JUL-20 6VFP 1 COMPND REMARK HETNAM LINK REVDAT 2 2 1 SITE ATOM REVDAT 1 11-MAR-20 6VFP 0 JRNL AUTH O.J.HARRISON,J.BRASCH,P.S.KATSAMBA,G.AHLSEN,A.J.NOBLE,H.DAN, JRNL AUTH 2 R.V.SAMPOGNA,C.S.POTTER,B.CARRAGHER,B.HONIG,L.SHAPIRO JRNL TITL FAMILY-WIDE STRUCTURAL AND BIOPHYSICAL ANALYSIS OF BINDING JRNL TITL 2 INTERACTIONS AMONG NON-CLUSTERED DELTA-PROTOCADHERINS. JRNL REF CELL REP V. 30 2655 2020 JRNL REFN ESSN 2211-1247 JRNL PMID 32101743 JRNL DOI 10.1016/J.CELREP.2020.02.003 REMARK 2 REMARK 2 RESOLUTION. 3.20 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) : 3.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.87 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 16561 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.224 REMARK 3 R VALUE (WORKING SET) : 0.222 REMARK 3 FREE R VALUE : 0.264 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 827 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 19.8686 - 5.7750 1.00 2782 145 0.1879 0.2171 REMARK 3 2 5.7750 - 4.6025 1.00 2643 140 0.2102 0.2558 REMARK 3 3 4.6025 - 4.0262 1.00 2594 138 0.2232 0.2737 REMARK 3 4 4.0262 - 3.6606 1.00 2587 137 0.2629 0.3056 REMARK 3 5 3.6606 - 3.3996 1.00 2573 134 0.3024 0.3674 REMARK 3 6 3.3996 - 3.2001 1.00 2555 133 0.3449 0.3921 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.538 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 32.550 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 115.5 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 144.6 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 3533 REMARK 3 ANGLE : 0.541 4749 REMARK 3 CHIRALITY : 0.045 560 REMARK 3 PLANARITY : 0.003 638 REMARK 3 DIHEDRAL : 10.322 2139 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 6VFP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-JAN-20. REMARK 100 THE DEPOSITION ID IS D_1000242932. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-APR-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 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-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9791 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16684 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.200 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 18.30 REMARK 200 R MERGE (I) : 0.12000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.42 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 19.10 REMARK 200 R MERGE FOR SHELL (I) : 1.68500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.100 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: 5DZQ, 4ZPL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 75.34 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.99 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 8.5% (W/V) PEG 4000, 20% (V/V) REMARK 280 GLYCEROL, 0.1M TRIS-BICINE BUFFER PH8.5, 0.02 M D-GLUCOSE, 0.02 REMARK 280 M D-MANNOSE, 0.02 M D-GALACTOSE, 0.02 M L-FUCOSE, 0.02 M D- REMARK 280 XYLOSE, 0.02 M N-ACETYL-D-GLUCOSAMINE, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 296K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 2 2 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 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+5/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-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 49.94867 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 99.89733 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 74.92300 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 124.87167 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 24.97433 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 49.94867 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 99.89733 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 124.87167 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 74.92300 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 24.97433 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: 4800 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 48810 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -84.0 KCAL/MOL 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 BIOMT1 2 0.500000 0.866025 0.000000 -74.29750 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 128.68704 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 324.66633 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 A 615 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 THR A 1 REMARK 465 ASP A 441 REMARK 465 HIS A 442 REMARK 465 HIS A 443 REMARK 465 HIS A 444 REMARK 465 HIS A 445 REMARK 465 HIS A 446 REMARK 465 HIS A 447 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 251 -167.77 -72.76 REMARK 500 ASP A 366 -166.79 -72.60 REMARK 500 GLN A 387 109.62 -59.62 REMARK 500 LEU A 435 118.45 -160.80 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 505 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 9 OE1 REMARK 620 2 GLU A 10 OE2 116.2 REMARK 620 3 ASP A 59 OD1 87.1 96.7 REMARK 620 4 GLU A 61 OE1 81.8 160.5 91.3 REMARK 620 5 ASP A 106 OD2 109.1 95.5 152.7 70.4 REMARK 620 6 HOH A 606 O 157.7 85.7 85.9 77.1 70.7 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 9 OE2 REMARK 620 2 GLU A 61 OE1 72.5 REMARK 620 3 GLU A 61 OE2 74.9 47.6 REMARK 620 4 ASP A 103 OD1 80.8 129.6 84.8 REMARK 620 5 ILE A 104 O 82.5 127.2 157.2 89.1 REMARK 620 6 ASP A 106 OD1 75.5 66.7 113.1 144.7 62.3 REMARK 620 7 ASP A 139 OD1 166.8 99.1 107.3 112.2 95.3 91.9 REMARK 620 N 1 2 3 4 5 6 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 105 OD1 REMARK 620 2 ASN A 107 O 88.3 REMARK 620 3 ASP A 137 OD1 147.6 81.4 REMARK 620 4 ASP A 137 OD2 157.5 105.7 54.0 REMARK 620 5 ASP A 139 OD2 71.9 73.0 75.7 128.6 REMARK 620 6 ASN A 143 O 88.2 161.4 91.9 83.8 88.5 REMARK 620 7 ASP A 197 OD2 66.2 100.5 145.9 93.5 137.8 94.8 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 122 OE1 REMARK 620 2 ASP A 182 OD1 100.2 REMARK 620 3 GLU A 184 OE1 89.8 89.1 REMARK 620 4 ASP A 218 OD2 106.4 153.4 90.9 REMARK 620 5 HOH A 603 O 164.0 65.8 82.5 87.8 REMARK 620 6 HOH A 607 O 119.2 87.4 151.0 79.9 69.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 510 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 122 OE2 REMARK 620 2 GLU A 184 OE1 93.8 REMARK 620 3 GLU A 184 OE2 108.0 45.7 REMARK 620 4 ASP A 215 OD1 85.4 145.7 102.0 REMARK 620 5 THR A 216 O 77.8 139.2 173.0 74.2 REMARK 620 6 ASP A 218 OD1 88.2 72.9 116.3 141.2 67.1 REMARK 620 7 ASP A 251 OD1 160.4 93.5 90.0 98.5 84.8 76.7 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 511 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 217 OD1 REMARK 620 2 ASN A 219 O 97.2 REMARK 620 3 ASP A 249 OD1 144.8 72.2 REMARK 620 4 ASP A 249 OD2 161.6 70.7 46.2 REMARK 620 5 ASP A 251 OD2 80.4 68.1 64.5 106.6 REMARK 620 6 ASN A 255 O 98.1 161.2 89.0 96.7 103.9 REMARK 620 7 ASP A 304 OD2 64.9 112.1 150.3 105.9 145.2 84.4 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 512 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 234 OE1 REMARK 620 2 GLU A 234 OE2 43.9 REMARK 620 3 GLU A 291 OE2 109.5 67.8 REMARK 620 4 ASP A 322 OD1 95.8 109.5 90.9 REMARK 620 5 MET A 323 O 82.8 125.4 166.5 82.1 REMARK 620 6 ASP A 325 OD1 79.6 76.6 103.4 165.7 83.9 REMARK 620 7 ASP A 366 OD1 153.1 146.1 93.2 98.2 76.5 81.2 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 513 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 234 OE2 REMARK 620 2 ASP A 289 OD1 94.1 REMARK 620 3 ASP A 289 OD2 137.1 47.7 REMARK 620 4 GLU A 291 OE1 83.5 84.6 106.9 REMARK 620 5 ASP A 325 OD2 88.2 177.7 130.3 95.5 REMARK 620 6 HOH A 604 O 115.5 109.0 71.3 154.8 70.1 REMARK 620 N 1 2 3 4 5 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 ASN A 324 OD1 REMARK 620 2 ASN A 326 O 95.4 REMARK 620 3 ASP A 364 OD1 163.5 68.5 REMARK 620 4 ASP A 364 OD2 132.3 110.7 55.5 REMARK 620 5 ASP A 366 OD2 65.5 72.3 104.5 84.9 REMARK 620 6 ASN A 370 O 88.5 162.5 105.8 55.9 94.2 REMARK 620 7 ASP A 423 OD2 68.7 115.1 120.6 126.6 134.0 82.1 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 514 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 408 OD1 REMARK 620 2 ASP A 408 OD2 43.4 REMARK 620 N 1 DBREF 6VFP A 1 441 UNP Q08174 PCDH1_HUMAN 58 498 SEQADV 6VFP HIS A 442 UNP Q08174 EXPRESSION TAG SEQADV 6VFP HIS A 443 UNP Q08174 EXPRESSION TAG SEQADV 6VFP HIS A 444 UNP Q08174 EXPRESSION TAG SEQADV 6VFP HIS A 445 UNP Q08174 EXPRESSION TAG SEQADV 6VFP HIS A 446 UNP Q08174 EXPRESSION TAG SEQADV 6VFP HIS A 447 UNP Q08174 EXPRESSION TAG SEQRES 1 A 447 THR ARG VAL VAL TYR LYS VAL PRO GLU GLU GLN PRO PRO SEQRES 2 A 447 ASN THR LEU ILE GLY SER LEU ALA ALA ASP TYR GLY PHE SEQRES 3 A 447 PRO ASP VAL GLY HIS LEU TYR LYS LEU GLU VAL GLY ALA SEQRES 4 A 447 PRO TYR LEU ARG VAL ASP GLY LYS THR GLY ASP ILE PHE SEQRES 5 A 447 THR THR GLU THR SER ILE ASP ARG GLU GLY LEU ARG GLU SEQRES 6 A 447 CYS GLN ASN GLN LEU PRO GLY ASP PRO CYS ILE LEU GLU SEQRES 7 A 447 PHE GLU VAL SER ILE THR ASP LEU VAL GLN ASN GLY SER SEQRES 8 A 447 PRO ARG LEU LEU GLU GLY GLN ILE GLU VAL GLN ASP ILE SEQRES 9 A 447 ASN ASP ASN THR PRO ASN PHE ALA SER PRO VAL ILE THR SEQRES 10 A 447 LEU ALA ILE PRO GLU ASN THR ASN ILE GLY SER LEU PHE SEQRES 11 A 447 PRO ILE PRO LEU ALA SER ASP ARG ASP ALA GLY PRO ASN SEQRES 12 A 447 GLY VAL ALA SER TYR GLU LEU GLN ALA GLY PRO GLU ALA SEQRES 13 A 447 GLN GLU LEU PHE GLY LEU GLN VAL ALA GLU ASP GLN GLU SEQRES 14 A 447 GLU LYS GLN PRO GLN LEU ILE VAL MET GLY ASN LEU ASP SEQRES 15 A 447 ARG GLU ARG TRP ASP SER TYR ASP LEU THR ILE LYS VAL SEQRES 16 A 447 GLN ASP GLY GLY SER PRO PRO ARG ALA SER SER ALA LEU SEQRES 17 A 447 LEU ARG VAL THR VAL LEU ASP THR ASN ASP ASN ALA PRO SEQRES 18 A 447 LYS PHE GLU ARG PRO SER TYR GLU ALA GLU LEU SER GLU SEQRES 19 A 447 ASN SER PRO ILE GLY HIS SER VAL ILE GLN VAL LYS ALA SEQRES 20 A 447 ASN ASP SER ASP GLN GLY ALA ASN ALA GLU ILE GLU TYR SEQRES 21 A 447 THR PHE HIS GLN ALA PRO GLU VAL VAL ARG ARG LEU LEU SEQRES 22 A 447 ARG LEU ASP ARG ASN THR GLY LEU ILE THR VAL GLN GLY SEQRES 23 A 447 PRO VAL ASP ARG GLU ASP LEU SER THR LEU ARG PHE SER SEQRES 24 A 447 VAL LEU ALA LYS ASP ARG GLY THR ASN PRO LYS SER ALA SEQRES 25 A 447 ARG ALA GLN VAL VAL VAL THR VAL LYS ASP MET ASN ASP SEQRES 26 A 447 ASN ALA PRO THR ILE GLU ILE ARG GLY ILE GLY LEU VAL SEQRES 27 A 447 THR HIS GLN ASP GLY MET ALA ASN ILE SER GLU ASP VAL SEQRES 28 A 447 ALA GLU GLU THR ALA VAL ALA LEU VAL GLN VAL SER ASP SEQRES 29 A 447 ARG ASP GLU GLY GLU ASN ALA ALA VAL THR CYS VAL VAL SEQRES 30 A 447 ALA GLY ASP VAL PRO PHE GLN LEU ARG GLN ALA SER GLU SEQRES 31 A 447 THR GLY SER ASP SER LYS LYS LYS TYR PHE LEU GLN THR SEQRES 32 A 447 THR THR PRO LEU ASP TYR GLU LYS VAL LYS ASP TYR THR SEQRES 33 A 447 ILE GLU ILE VAL ALA VAL ASP SER GLY ASN PRO PRO LEU SEQRES 34 A 447 SER SER THR ASN SER LEU LYS VAL GLN VAL VAL ASP HIS SEQRES 35 A 447 HIS HIS HIS HIS HIS HET NAG B 1 26 HET NAG B 2 26 HET BMA B 3 21 HET NAG A 504 14 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 CA A 510 1 HET CA A 511 1 HET CA A 512 1 HET CA A 513 1 HET CA A 514 1 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM BMA BETA-D-MANNOPYRANOSE HETNAM CA CALCIUM ION 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 HETSYN BMA BETA-D-MANNOSE; D-MANNOSE; MANNOSE FORMUL 2 NAG 3(C8 H15 N O6) FORMUL 2 BMA C6 H12 O6 FORMUL 4 CA 10(CA 2+) FORMUL 14 HOH *15(H2 O) HELIX 1 AA1 ALA A 21 ASP A 23 5 3 HELIX 2 AA2 LEU A 63 GLN A 67 5 5 HELIX 3 AA3 ALA A 140 ASN A 143 5 4 HELIX 4 AA4 GLN A 252 ALA A 256 5 5 HELIX 5 AA5 PRO A 266 LEU A 272 1 7 HELIX 6 AA6 GLU A 367 ALA A 371 5 5 SHEET 1 AA1 4 VAL A 4 PRO A 8 0 SHEET 2 AA1 4 ARG A 93 GLN A 102 1 O GLN A 102 N VAL A 7 SHEET 3 AA1 4 CYS A 75 ASP A 85 -1 N CYS A 75 O VAL A 101 SHEET 4 AA1 4 HIS A 31 LEU A 35 -1 N LYS A 34 O SER A 82 SHEET 1 AA2 3 LEU A 16 SER A 19 0 SHEET 2 AA2 3 ASP A 50 PHE A 52 -1 O ILE A 51 N GLY A 18 SHEET 3 AA2 3 ARG A 43 VAL A 44 -1 N ARG A 43 O PHE A 52 SHEET 1 AA3 4 VAL A 115 PRO A 121 0 SHEET 2 AA3 4 ALA A 204 LEU A 214 1 O ARG A 210 N ILE A 116 SHEET 3 AA3 4 SER A 188 ASP A 197 -1 N ILE A 193 O ALA A 207 SHEET 4 AA3 4 VAL A 145 ALA A 152 -1 N GLN A 151 O THR A 192 SHEET 1 AA4 3 LEU A 129 PRO A 131 0 SHEET 2 AA4 3 GLU A 170 VAL A 177 -1 O LEU A 175 N PHE A 130 SHEET 3 AA4 3 PHE A 160 ASP A 167 -1 N GLN A 163 O GLN A 174 SHEET 1 AA5 2 LYS A 222 PHE A 223 0 SHEET 2 AA5 2 ALA A 247 ASN A 248 -1 O ASN A 248 N LYS A 222 SHEET 1 AA6 4 SER A 227 SER A 233 0 SHEET 2 AA6 4 SER A 311 LYS A 321 1 O LYS A 321 N LEU A 232 SHEET 3 AA6 4 THR A 295 ASP A 304 -1 N LEU A 296 O VAL A 318 SHEET 4 AA6 4 ILE A 258 HIS A 263 -1 N THR A 261 O LEU A 301 SHEET 1 AA7 3 SER A 241 GLN A 244 0 SHEET 2 AA7 3 LEU A 281 VAL A 284 -1 O ILE A 282 N ILE A 243 SHEET 3 AA7 3 LEU A 273 LEU A 275 -1 N ARG A 274 O THR A 283 SHEET 1 AA8 4 THR A 329 GLY A 334 0 SHEET 2 AA8 4 ALA A 356 SER A 363 -1 O LEU A 359 N ARG A 333 SHEET 3 AA8 4 LYS A 397 THR A 403 -1 O LEU A 401 N VAL A 357 SHEET 4 AA8 4 PHE A 383 GLN A 387 -1 N ARG A 386 O PHE A 400 SHEET 1 AA9 4 MET A 344 SER A 348 0 SHEET 2 AA9 4 SER A 430 VAL A 440 1 O GLN A 438 N ALA A 345 SHEET 3 AA9 4 ILE A 417 ASP A 423 -1 N ILE A 419 O ASN A 433 SHEET 4 AA9 4 VAL A 373 VAL A 377 -1 N THR A 374 O VAL A 422 SSBOND 1 CYS A 66 CYS A 75 1555 1555 2.03 LINK ND2 ASN A 248 C1 NAG B 1 1555 1555 1.44 LINK ND2 ASN A 346 C1 NAG A 504 1555 1555 1.45 LINK O4 NAG B 1 C1 NAG B 2 1555 1555 1.44 LINK O4 NAG B 2 C1 BMA B 3 1555 1555 1.45 LINK OE1 GLU A 9 CA CA A 505 1555 1555 2.39 LINK OE2 GLU A 9 CA CA A 509 1555 1555 2.43 LINK OE2 GLU A 10 CA CA A 505 1555 1555 2.41 LINK OD1 ASP A 59 CA CA A 505 1555 1555 2.36 LINK OE1 GLU A 61 CA CA A 505 1555 1555 2.29 LINK OE1 GLU A 61 CA CA A 509 1555 1555 2.94 LINK OE2 GLU A 61 CA CA A 509 1555 1555 2.31 LINK OD1 ASP A 103 CA CA A 509 1555 1555 2.28 LINK O ILE A 104 CA CA A 509 1555 1555 2.36 LINK OD1 ASN A 105 CA CA A 507 1555 1555 2.41 LINK OD2 ASP A 106 CA CA A 505 1555 1555 2.32 LINK OD1 ASP A 106 CA CA A 509 1555 1555 2.27 LINK O ASN A 107 CA CA A 507 1555 1555 2.40 LINK OE1 GLU A 122 CA CA A 506 1555 1555 2.37 LINK OE2 GLU A 122 CA CA A 510 1555 1555 2.36 LINK OD1 ASP A 137 CA CA A 507 1555 1555 2.48 LINK OD2 ASP A 137 CA CA A 507 1555 1555 2.33 LINK OD2 ASP A 139 CA CA A 507 1555 1555 2.33 LINK OD1 ASP A 139 CA CA A 509 1555 1555 2.36 LINK O ASN A 143 CA CA A 507 1555 1555 2.40 LINK OD1 ASP A 182 CA CA A 506 1555 1555 2.30 LINK OE1 GLU A 184 CA CA A 506 1555 1555 2.28 LINK OE1 GLU A 184 CA CA A 510 1555 1555 3.04 LINK OE2 GLU A 184 CA CA A 510 1555 1555 2.38 LINK OD2 ASP A 197 CA CA A 507 1555 1555 2.42 LINK OD1 ASP A 215 CA CA A 510 1555 1555 2.32 LINK O THR A 216 CA CA A 510 1555 1555 2.47 LINK OD1 ASN A 217 CA CA A 511 1555 1555 2.35 LINK OD2 ASP A 218 CA CA A 506 1555 1555 2.23 LINK OD1 ASP A 218 CA CA A 510 1555 1555 2.29 LINK O ASN A 219 CA CA A 511 1555 1555 2.37 LINK OE1 GLU A 234 CA CA A 512 1555 1555 2.41 LINK OE2 GLU A 234 CA CA A 512 1555 1555 3.15 LINK OE2 GLU A 234 CA CA A 513 1555 1555 2.25 LINK OD1 ASP A 249 CA CA A 511 1555 1555 3.04 LINK OD2 ASP A 249 CA CA A 511 1555 1555 2.24 LINK OD1 ASP A 251 CA CA A 510 1555 1555 2.41 LINK OD2 ASP A 251 CA CA A 511 1555 1555 2.35 LINK O ASN A 255 CA CA A 511 1555 1555 2.32 LINK OD1 ASP A 289 CA CA A 513 1555 1555 2.32 LINK OD2 ASP A 289 CA CA A 513 1555 1555 2.93 LINK OE2 GLU A 291 CA CA A 512 1555 1555 2.29 LINK OE1 GLU A 291 CA CA A 513 1555 1555 2.31 LINK OD2 ASP A 304 CA CA A 511 1555 1555 2.35 LINK OD1 ASP A 322 CA CA A 512 1555 1555 2.34 LINK O MET A 323 CA CA A 512 1555 1555 2.16 LINK OD1 ASN A 324 CA CA A 508 1555 1555 2.39 LINK OD1 ASP A 325 CA CA A 512 1555 1555 2.30 LINK OD2 ASP A 325 CA CA A 513 1555 1555 2.22 LINK O ASN A 326 CA CA A 508 1555 1555 2.37 LINK OD1 ASP A 364 CA CA A 508 1555 1555 2.34 LINK OD2 ASP A 364 CA CA A 508 1555 1555 2.37 LINK OD2 ASP A 366 CA CA A 508 1555 1555 2.42 LINK OD1 ASP A 366 CA CA A 512 1555 1555 2.41 LINK O ASN A 370 CA CA A 508 1555 1555 2.43 LINK OD1 ASP A 408 CA CA A 514 1555 1555 2.80 LINK OD2 ASP A 408 CA CA A 514 1555 1555 3.09 LINK OD2 ASP A 423 CA CA A 508 1555 1555 2.33 LINK CA CA A 505 O HOH A 606 1555 1555 2.45 LINK CA CA A 506 O HOH A 603 1555 1555 2.43 LINK CA CA A 506 O HOH A 607 1555 1555 2.40 LINK CA CA A 513 O HOH A 604 1555 1555 2.33 CISPEP 1 SER A 200 PRO A 201 0 -3.02 CISPEP 2 ASN A 426 PRO A 427 0 1.01 CRYST1 148.595 148.595 149.846 90.00 90.00 120.00 P 61 2 2 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 0.006730 0.003885 0.000000 0.00000 SCALE2 0.000000 0.007771 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006674 0.00000