HEADER CELL ADHESION 04-MAY-15 4ZMW
TITLE CRYSTAL STRUCTURE OF HUMAN P-CADHERIN (ENC-X-DIMER)
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: CADHERIN-3;
COMPND 3 CHAIN: A, B;
COMPND 4 FRAGMENT: UNP RESIDUES 108-320;
COMPND 5 SYNONYM: PLACENTAL CADHERIN,P-CADHERIN;
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: CDH3, CDHP;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008;
SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3);
SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 10 EXPRESSION_SYSTEM_PLASMID: CHAMPION PET SUMO
KEYWDS DIMERIZATION, CONFORMATIONAL CHANGE, CELL ADHESION
EXPDTA X-RAY DIFFRACTION
AUTHOR J.M.M.CAAVEIRO,S.KUDO,K.TSUMOTO
REVDAT 4 08-NOV-23 4ZMW 1 LINK
REVDAT 3 19-FEB-20 4ZMW 1 JRNL REMARK
REVDAT 2 21-SEP-16 4ZMW 1 JRNL
REVDAT 1 07-SEP-16 4ZMW 0
JRNL AUTH S.KUDO,J.M.CAAVEIRO,K.TSUMOTO
JRNL TITL ADHESIVE DIMERIZATION OF HUMAN P-CADHERIN CATALYZED BY A
JRNL TITL 2 CHAPERONE-LIKE MECHANISM
JRNL REF STRUCTURE V. 24 1523 2016
JRNL REFN ISSN 0969-2126
JRNL PMID 27545624
JRNL DOI 10.1016/J.STR.2016.07.002
REMARK 2
REMARK 2 RESOLUTION. 2.30 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.8.0073
REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER,
REMARK 3 : NICHOLLS,WINN,LONG,VAGIN
REMARK 3
REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.02
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7
REMARK 3 NUMBER OF REFLECTIONS : 31831
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT
REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM
REMARK 3 R VALUE (WORKING + TEST SET) : 0.233
REMARK 3 R VALUE (WORKING SET) : 0.230
REMARK 3 FREE R VALUE : 0.276
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.300
REMARK 3 FREE R VALUE TEST SET COUNT : 1798
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : 20
REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.30
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.36
REMARK 3 REFLECTION IN BIN (WORKING SET) : 2111
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 88.11
REMARK 3 BIN R VALUE (WORKING SET) : 0.2660
REMARK 3 BIN FREE R VALUE SET COUNT : 98
REMARK 3 BIN FREE R VALUE : 0.2570
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 3274
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 41
REMARK 3 SOLVENT ATOMS : 102
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.49
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -0.71000
REMARK 3 B22 (A**2) : -2.43000
REMARK 3 B33 (A**2) : 3.05000
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : 0.29000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): 0.236
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.213
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.162
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.571
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.910
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.862
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3390 ; 0.013 ; 0.019
REMARK 3 BOND LENGTHS OTHERS (A): 3125 ; 0.001 ; 0.020
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4622 ; 1.592 ; 1.961
REMARK 3 BOND ANGLES OTHERS (DEGREES): 7252 ; 0.804 ; 3.000
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 430 ; 7.007 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 151 ;37.326 ;25.762
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 549 ;15.766 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 12 ;10.384 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 536 ; 0.088 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3789 ; 0.007 ; 0.021
REMARK 3 GENERAL PLANES OTHERS (A): 691 ; 0.001 ; 0.020
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1708 ; 2.569 ; 3.557
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1707 ; 2.568 ; 3.556
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2133 ; 4.062 ; 5.322
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2134 ; 4.061 ; 5.323
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1682 ; 3.278 ; 3.970
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1652 ; 2.805 ; 3.933
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2444 ; 4.471 ; 5.750
REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3554 ; 6.799 ;27.894
REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3522 ; 6.700 ;27.912
REMARK 3
REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL
REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3
REMARK 3 NCS RESTRAINTS STATISTICS
REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : NULL
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : MASK
REMARK 3 PARAMETERS FOR MASK CALCULATION
REMARK 3 VDW PROBE RADIUS : 1.20
REMARK 3 ION PROBE RADIUS : 0.80
REMARK 3 SHRINKAGE RADIUS : 0.80
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING
REMARK 3 POSITIONS
REMARK 4
REMARK 4 4ZMW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 16-MAY-15.
REMARK 100 THE DEPOSITION ID IS D_1000209556.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 04-NOV-14
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 8.5
REMARK 200 NUMBER OF CRYSTALS USED : NULL
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : PHOTON FACTORY
REMARK 200 BEAMLINE : BL-5A
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.000
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 : MOSFLM
REMARK 200 DATA SCALING SOFTWARE : SCALA
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33629
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300
REMARK 200 RESOLUTION RANGE LOW (A) : 47.020
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8
REMARK 200 DATA REDUNDANCY : 5.000
REMARK 200 R MERGE (I) : 0.06600
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.4000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.42
REMARK 200 COMPLETENESS FOR SHELL (%) : 92.0
REMARK 200 DATA REDUNDANCY IN SHELL : 4.30
REMARK 200 R MERGE FOR SHELL (I) : 0.27900
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.800
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: 4ZMN
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 70.44
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.16
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 1.15 M LITHIUM SULFATE 7.5 MM NICKEL
REMARK 280 SULFATE 100 MM TRIS, PH 8.5, VAPOR DIFFUSION, HANGING DROP,
REMARK 280 TEMPERATURE 293K
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 47.18450
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 53.40500
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 47.18450
REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 53.40500
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: DIMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 2700 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 22020 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -141.0 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 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 MET A 0
REMARK 465 MET B 0
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 TRP A 2 66.49 -101.01
REMARK 500 ASN A 12 48.70 38.74
REMARK 500 ALA A 43 -76.98 -102.48
REMARK 500 LYS A 156 46.93 -96.38
REMARK 500 ASP A 180 103.68 -173.34
REMARK 500 ALA B 43 -79.70 -106.52
REMARK 500 LYS B 156 31.06 -97.05
REMARK 500 HIS B 159 -169.88 -125.30
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 301 CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 GLU A 11 OE2
REMARK 620 2 GLU A 69 OE1 83.3
REMARK 620 3 GLU A 69 OE2 106.8 50.2
REMARK 620 4 ASP A 100 OD1 83.6 117.9 77.0
REMARK 620 5 GLN A 101 O 80.4 147.2 162.6 88.4
REMARK 620 6 ASP A 103 OD1 90.9 78.3 121.1 161.9 73.7
REMARK 620 7 ASP A 136 OD1 165.6 97.7 84.4 108.1 91.5 75.4
REMARK 620 N 1 2 3 4 5 6
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 CA A 302 CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASN A 102 OD1
REMARK 620 2 HIS A 104 O 95.8
REMARK 620 3 ASP A 134 OD1 157.1 86.6
REMARK 620 4 ASP A 134 OD2 148.5 96.6 52.7
REMARK 620 5 ASP A 136 OD2 73.2 80.6 129.5 80.4
REMARK 620 6 ASN A 143 O 84.9 176.2 91.4 84.7 103.1
REMARK 620 7 ASP A 195 OD2 79.6 79.6 78.4 131.2 144.3 96.8
REMARK 620 N 1 2 3 4 5 6
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 NI A 305 NI
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HIS A 104 NE2
REMARK 620 2 SO4 A 303 S 149.0
REMARK 620 3 SO4 A 303 O1 111.5 40.3
REMARK 620 4 SO4 A 303 O4 144.5 39.5 76.1
REMARK 620 5 SO4 A 304 S 82.6 122.0 125.1 122.6
REMARK 620 6 SO4 A 304 O3 93.0 98.5 90.3 122.1 34.9
REMARK 620 7 SO4 A 304 O4 73.6 137.3 159.2 112.0 34.2 69.1
REMARK 620 8 HOH A 403 O 83.2 100.6 120.2 64.4 114.0 148.6 80.0
REMARK 620 N 1 2 3 4 5 6 7
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 CA B 301 CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 GLU B 11 OE2
REMARK 620 2 GLU B 69 OE1 86.1
REMARK 620 3 GLU B 69 OE2 113.4 48.8
REMARK 620 4 ASP B 100 OD1 85.0 118.9 81.1
REMARK 620 5 GLN B 101 O 85.3 151.1 157.0 87.7
REMARK 620 6 ASP B 103 OD1 90.5 78.3 116.8 161.7 74.2
REMARK 620 7 ASP B 136 OD1 160.9 96.3 81.6 110.0 83.5 71.5
REMARK 620 N 1 2 3 4 5 6
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 CA B 302 CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASN B 102 OD1
REMARK 620 2 HIS B 104 O 97.8
REMARK 620 3 ASP B 134 OD1 151.0 95.4
REMARK 620 4 ASP B 134 OD2 151.0 96.8 50.6
REMARK 620 5 ASP B 136 OD2 77.6 76.5 130.8 81.8
REMARK 620 6 ASN B 143 O 82.0 177.5 85.9 82.3 101.0
REMARK 620 7 ASP B 195 OD2 76.9 81.2 79.8 130.2 143.2 101.1
REMARK 620 N 1 2 3 4 5 6
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 NI B 308 NI
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HIS B 104 NE2
REMARK 620 2 SO4 B 306 S 88.2
REMARK 620 3 SO4 B 306 O1 98.2 33.8
REMARK 620 4 SO4 B 306 O2 85.5 33.1 66.4
REMARK 620 5 SO4 B 307 S 129.8 132.7 104.4 144.7
REMARK 620 6 SO4 B 307 O1 93.9 169.5 135.8 157.4 40.5
REMARK 620 7 SO4 B 307 O3 165.6 106.2 94.2 106.2 38.7 72.0
REMARK 620 8 SO4 B 307 O4 117.0 109.5 76.2 139.0 33.8 60.4 59.2
REMARK 620 N 1 2 3 4 5 6 7
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 301
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 302
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 303
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 304
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue NI A 305
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue CA B 301
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC7
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue CA B 302
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC8
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 303
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC9
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 304
REMARK 800
REMARK 800 SITE_IDENTIFIER: AD1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 305
REMARK 800
REMARK 800 SITE_IDENTIFIER: AD2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 306
REMARK 800
REMARK 800 SITE_IDENTIFIER: AD3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 307
REMARK 800
REMARK 800 SITE_IDENTIFIER: AD4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue NI B 308
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 4ZML RELATED DB: PDB
REMARK 900 RELATED ID: 4ZMN RELATED DB: PDB
REMARK 900 RELATED ID: 4ZMO RELATED DB: PDB
REMARK 900 RELATED ID: 4ZMP RELATED DB: PDB
REMARK 900 RELATED ID: 4ZMQ RELATED DB: PDB
REMARK 900 RELATED ID: 4ZMT RELATED DB: PDB
REMARK 900 RELATED ID: 4ZMV RELATED DB: PDB
REMARK 900 RELATED ID: 4ZMX RELATED DB: PDB
REMARK 900 RELATED ID: 4ZMY RELATED DB: PDB
REMARK 900 RELATED ID: 4ZMZ RELATED DB: PDB
DBREF 4ZMW A 1 213 UNP P22223 CADH3_HUMAN 108 320
DBREF 4ZMW B 1 213 UNP P22223 CADH3_HUMAN 108 320
SEQADV 4ZMW MET A 0 UNP P22223 INITIATING METHIONINE
SEQADV 4ZMW VAL A 22 UNP P22223 ASN 129 ENGINEERED MUTATION
SEQADV 4ZMW MET B 0 UNP P22223 INITIATING METHIONINE
SEQADV 4ZMW VAL B 22 UNP P22223 ASN 129 ENGINEERED MUTATION
SEQRES 1 A 214 MET ASP TRP VAL VAL ALA PRO ILE SER VAL PRO GLU ASN
SEQRES 2 A 214 GLY LYS GLY PRO PHE PRO GLN ARG LEU VAL GLN LEU LYS
SEQRES 3 A 214 SER ASN LYS ASP ARG ASP THR LYS ILE PHE TYR SER ILE
SEQRES 4 A 214 THR GLY PRO GLY ALA ASP SER PRO PRO GLU GLY VAL PHE
SEQRES 5 A 214 ALA VAL GLU LYS GLU THR GLY TRP LEU LEU LEU ASN LYS
SEQRES 6 A 214 PRO LEU ASP ARG GLU GLU ILE ALA LYS TYR GLU LEU PHE
SEQRES 7 A 214 GLY HIS ALA VAL SER GLU ASN GLY ALA SER VAL GLU ASP
SEQRES 8 A 214 PRO MET ASN ILE SER ILE ILE VAL THR ASP GLN ASN ASP
SEQRES 9 A 214 HIS LYS PRO LYS PHE THR GLN ASP THR PHE ARG GLY SER
SEQRES 10 A 214 VAL LEU GLU GLY VAL LEU PRO GLY THR SER VAL MET GLN
SEQRES 11 A 214 VAL THR ALA THR ASP GLU ASP ASP ALA ILE TYR THR TYR
SEQRES 12 A 214 ASN GLY VAL VAL ALA TYR SER ILE HIS SER GLN GLU PRO
SEQRES 13 A 214 LYS ASP PRO HIS ASP LEU MET PHE THR ILE HIS ARG SER
SEQRES 14 A 214 THR GLY THR ILE SER VAL ILE SER SER GLY LEU ASP ARG
SEQRES 15 A 214 GLU LYS VAL PRO GLU TYR THR LEU THR ILE GLN ALA THR
SEQRES 16 A 214 ASP MET ASP GLY ASP GLY SER THR THR THR ALA VAL ALA
SEQRES 17 A 214 VAL VAL GLU ILE LEU ASP
SEQRES 1 B 214 MET ASP TRP VAL VAL ALA PRO ILE SER VAL PRO GLU ASN
SEQRES 2 B 214 GLY LYS GLY PRO PHE PRO GLN ARG LEU VAL GLN LEU LYS
SEQRES 3 B 214 SER ASN LYS ASP ARG ASP THR LYS ILE PHE TYR SER ILE
SEQRES 4 B 214 THR GLY PRO GLY ALA ASP SER PRO PRO GLU GLY VAL PHE
SEQRES 5 B 214 ALA VAL GLU LYS GLU THR GLY TRP LEU LEU LEU ASN LYS
SEQRES 6 B 214 PRO LEU ASP ARG GLU GLU ILE ALA LYS TYR GLU LEU PHE
SEQRES 7 B 214 GLY HIS ALA VAL SER GLU ASN GLY ALA SER VAL GLU ASP
SEQRES 8 B 214 PRO MET ASN ILE SER ILE ILE VAL THR ASP GLN ASN ASP
SEQRES 9 B 214 HIS LYS PRO LYS PHE THR GLN ASP THR PHE ARG GLY SER
SEQRES 10 B 214 VAL LEU GLU GLY VAL LEU PRO GLY THR SER VAL MET GLN
SEQRES 11 B 214 VAL THR ALA THR ASP GLU ASP ASP ALA ILE TYR THR TYR
SEQRES 12 B 214 ASN GLY VAL VAL ALA TYR SER ILE HIS SER GLN GLU PRO
SEQRES 13 B 214 LYS ASP PRO HIS ASP LEU MET PHE THR ILE HIS ARG SER
SEQRES 14 B 214 THR GLY THR ILE SER VAL ILE SER SER GLY LEU ASP ARG
SEQRES 15 B 214 GLU LYS VAL PRO GLU TYR THR LEU THR ILE GLN ALA THR
SEQRES 16 B 214 ASP MET ASP GLY ASP GLY SER THR THR THR ALA VAL ALA
SEQRES 17 B 214 VAL VAL GLU ILE LEU ASP
HET CA A 301 1
HET CA A 302 1
HET SO4 A 303 5
HET SO4 A 304 5
HET NI A 305 1
HET CA B 301 1
HET CA B 302 1
HET SO4 B 303 5
HET SO4 B 304 5
HET SO4 B 305 5
HET SO4 B 306 5
HET SO4 B 307 5
HET NI B 308 1
HETNAM CA CALCIUM ION
HETNAM SO4 SULFATE ION
HETNAM NI NICKEL (II) ION
FORMUL 3 CA 4(CA 2+)
FORMUL 5 SO4 7(O4 S 2-)
FORMUL 7 NI 2(NI 2+)
FORMUL 16 HOH *102(H2 O)
HELIX 1 AA1 SER A 26 ASP A 31 5 6
HELIX 2 AA2 MET A 196 ASP A 199 5 4
HELIX 3 AA3 SER B 26 ASP B 31 5 6
HELIX 4 AA4 MET B 196 ASP B 199 5 4
SHEET 1 AA1 4 ILE A 7 PRO A 10 0
SHEET 2 AA1 4 MET A 92 THR A 99 1 O ILE A 97 N ILE A 7
SHEET 3 AA1 4 LYS A 73 SER A 82 -1 N GLY A 78 O MET A 92
SHEET 4 AA1 4 ILE A 34 THR A 39 -1 N PHE A 35 O VAL A 81
SHEET 1 AA2 3 GLN A 19 GLN A 23 0
SHEET 2 AA2 3 TRP A 59 LEU A 62 -1 O LEU A 60 N VAL A 22
SHEET 3 AA2 3 PHE A 51 VAL A 53 -1 N ALA A 52 O LEU A 61
SHEET 1 AA3 2 LYS A 107 PHE A 108 0
SHEET 2 AA3 2 ALA A 132 THR A 133 -1 O THR A 133 N LYS A 107
SHEET 1 AA4 4 THR A 112 LEU A 118 0
SHEET 2 AA4 4 THR A 202 LEU A 212 1 O LEU A 212 N VAL A 117
SHEET 3 AA4 4 GLU A 186 THR A 194 -1 N LEU A 189 O ALA A 207
SHEET 4 AA4 4 ALA A 147 GLU A 154 -1 N SER A 152 O THR A 190
SHEET 1 AA5 3 SER A 126 GLN A 129 0
SHEET 2 AA5 3 THR A 171 VAL A 174 -1 O ILE A 172 N MET A 128
SHEET 3 AA5 3 PHE A 163 ILE A 165 -1 N THR A 164 O SER A 173
SHEET 1 AA6 4 ILE B 7 PRO B 10 0
SHEET 2 AA6 4 MET B 92 THR B 99 1 O ILE B 97 N ILE B 7
SHEET 3 AA6 4 LYS B 73 SER B 82 -1 N LEU B 76 O ILE B 94
SHEET 4 AA6 4 ILE B 34 THR B 39 -1 N SER B 37 O HIS B 79
SHEET 1 AA7 3 GLN B 19 GLN B 23 0
SHEET 2 AA7 3 TRP B 59 LEU B 62 -1 O LEU B 60 N VAL B 22
SHEET 3 AA7 3 PHE B 51 VAL B 53 -1 N ALA B 52 O LEU B 61
SHEET 1 AA8 2 LYS B 107 PHE B 108 0
SHEET 2 AA8 2 ALA B 132 THR B 133 -1 O THR B 133 N LYS B 107
SHEET 1 AA9 4 THR B 112 LEU B 118 0
SHEET 2 AA9 4 THR B 202 LEU B 212 1 O GLU B 210 N GLY B 115
SHEET 3 AA9 4 GLU B 186 THR B 194 -1 N LEU B 189 O ALA B 207
SHEET 4 AA9 4 ALA B 147 GLU B 154 -1 N SER B 152 O THR B 190
SHEET 1 AB1 3 SER B 126 GLN B 129 0
SHEET 2 AB1 3 THR B 171 VAL B 174 -1 O ILE B 172 N VAL B 127
SHEET 3 AB1 3 PHE B 163 ILE B 165 -1 N THR B 164 O SER B 173
LINK OE2 GLU A 11 CA CA A 301 1555 1555 2.31
LINK OE1 GLU A 69 CA CA A 301 1555 1555 2.73
LINK OE2 GLU A 69 CA CA A 301 1555 1555 2.33
LINK OD1 ASP A 100 CA CA A 301 1555 1555 2.30
LINK O GLN A 101 CA CA A 301 1555 1555 2.39
LINK OD1 ASN A 102 CA CA A 302 1555 1555 2.23
LINK OD1 ASP A 103 CA CA A 301 1555 1555 2.32
LINK O HIS A 104 CA CA A 302 1555 1555 2.24
LINK NE2 HIS A 104 NI NI A 305 1555 1555 2.19
LINK OD1 ASP A 134 CA CA A 302 1555 1555 2.49
LINK OD2 ASP A 134 CA CA A 302 1555 1555 2.36
LINK OD1 ASP A 136 CA CA A 301 1555 1555 2.42
LINK OD2 ASP A 136 CA CA A 302 1555 1555 2.30
LINK O ASN A 143 CA CA A 302 1555 1555 2.36
LINK OD2 ASP A 195 CA CA A 302 1555 1555 2.22
LINK S SO4 A 303 NI NI A 305 1555 1555 2.30
LINK O1 SO4 A 303 NI NI A 305 1555 1555 1.87
LINK O4 SO4 A 303 NI NI A 305 1555 1555 2.02
LINK S SO4 A 304 NI NI A 305 1555 1555 2.63
LINK O3 SO4 A 304 NI NI A 305 1555 1555 2.43
LINK O4 SO4 A 304 NI NI A 305 1555 1555 1.85
LINK NI NI A 305 O HOH A 403 1555 1555 2.61
LINK OE2 GLU B 11 CA CA B 301 1555 1555 2.25
LINK OE1 GLU B 69 CA CA B 301 1555 1555 2.77
LINK OE2 GLU B 69 CA CA B 301 1555 1555 2.35
LINK OD1 ASP B 100 CA CA B 301 1555 1555 2.27
LINK O GLN B 101 CA CA B 301 1555 1555 2.43
LINK OD1 ASN B 102 CA CA B 302 1555 1555 2.22
LINK OD1 ASP B 103 CA CA B 301 1555 1555 2.31
LINK O HIS B 104 CA CA B 302 1555 1555 2.28
LINK NE2 HIS B 104 NI NI B 308 1555 1555 2.12
LINK OD1 ASP B 134 CA CA B 302 1555 1555 2.60
LINK OD2 ASP B 134 CA CA B 302 1555 1555 2.63
LINK OD1 ASP B 136 CA CA B 301 1555 1555 2.25
LINK OD2 ASP B 136 CA CA B 302 1555 1555 2.49
LINK O ASN B 143 CA CA B 302 1555 1555 2.29
LINK OD2 ASP B 195 CA CA B 302 1555 1555 2.33
LINK S SO4 B 306 NI NI B 308 1555 1555 2.66
LINK O1 SO4 B 306 NI NI B 308 1555 1555 2.49
LINK O2 SO4 B 306 NI NI B 308 1555 1555 1.87
LINK S SO4 B 307 NI NI B 308 1555 1555 2.27
LINK O1 SO4 B 307 NI NI B 308 1555 1555 1.98
LINK O3 SO4 B 307 NI NI B 308 1555 1555 2.22
LINK O4 SO4 B 307 NI NI B 308 1555 1555 2.65
CISPEP 1 GLY A 15 PRO A 16 0 11.58
CISPEP 2 PHE A 17 PRO A 18 0 5.20
CISPEP 3 PRO A 46 PRO A 47 0 -4.34
CISPEP 4 GLU A 154 PRO A 155 0 -5.36
CISPEP 5 ASP A 157 PRO A 158 0 6.72
CISPEP 6 GLY B 15 PRO B 16 0 10.91
CISPEP 7 PHE B 17 PRO B 18 0 3.88
CISPEP 8 PRO B 46 PRO B 47 0 -5.15
CISPEP 9 GLU B 154 PRO B 155 0 -15.02
CISPEP 10 ASP B 157 PRO B 158 0 6.29
SITE 1 AC1 6 GLU A 11 GLU A 69 ASP A 100 GLN A 101
SITE 2 AC1 6 ASP A 103 ASP A 136
SITE 1 AC2 6 ASN A 102 HIS A 104 ASP A 134 ASP A 136
SITE 2 AC2 6 ASN A 143 ASP A 195
SITE 1 AC3 6 ASP A 67 GLU A 69 HIS A 104 SO4 A 304
SITE 2 AC3 6 NI A 305 HOH A 403
SITE 1 AC4 6 ASP A 67 ASP A 103 HIS A 104 SO4 A 303
SITE 2 AC4 6 NI A 305 HOH A 403
SITE 1 AC5 4 HIS A 104 SO4 A 303 SO4 A 304 HOH A 403
SITE 1 AC6 6 GLU B 11 GLU B 69 ASP B 100 GLN B 101
SITE 2 AC6 6 ASP B 103 ASP B 136
SITE 1 AC7 6 ASN B 102 HIS B 104 ASP B 134 ASP B 136
SITE 2 AC7 6 ASN B 143 ASP B 195
SITE 1 AC8 7 ARG A 68 GLU A 135 HOH A 401 GLN B 110
SITE 2 AC8 7 PHE B 113 ARG B 114 HOH B 427
SITE 1 AC9 2 ARG A 181 ARG B 20
SITE 1 AD1 4 THR B 32 SER B 82 ASN B 84 ALA B 86
SITE 1 AD2 5 ASP B 67 ASP B 103 HIS B 104 SO4 B 307
SITE 2 AD2 5 NI B 308
SITE 1 AD3 5 ASP B 67 HIS B 104 GLU B 135 SO4 B 306
SITE 2 AD3 5 NI B 308
SITE 1 AD4 3 HIS B 104 SO4 B 306 SO4 B 307
CRYST1 94.369 106.810 77.579 90.00 94.86 90.00 C 1 2 1 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 0.010597 0.000000 0.000901 0.00000
SCALE2 0.000000 0.009362 0.000000 0.00000
SCALE3 0.000000 0.000000 0.012937 0.00000
(ATOM LINES ARE NOT SHOWN.)
END