HEADER HORMONE 02-FEB-16 5FV2 TITLE CRYSTAL STRUCTURE OF HVEGF IN COMPLEX WITH VH DOMAIN ANTIBODY COMPND MOL_ID: 1; COMPND 2 MOLECULE: VH DOMAIN ANTIBODY; COMPND 3 CHAIN: A, B, C; COMPND 4 FRAGMENT: VH DOMAIN ANTIBODY; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: VASCULAR ENDOTHELIAL GROWTH FACTOR; COMPND 8 CHAIN: V, W, X; COMPND 9 FRAGMENT: VEGF UNP RESIDUES 27-136; COMPND 10 SYNONYM: VEGF-A, VASCULAR PERMEABILITY FACTOR, VPF, VASCULAR COMPND 11 ENDOTHELIAL GROWTH FACTOR; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 9 ORGANISM_COMMON: HUMAN; SOURCE 10 ORGANISM_TAXID: 9606; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HORMONE, GROWTH FACTOR RECEPTOR, VEGF, DOMAIN ANTIBODY, VASCULAR KEYWDS 2 ENDOTHELIAL GROWTH FACTOR EXPDTA X-RAY DIFFRACTION AUTHOR C.CHUNG,T.BATUWANGALA REVDAT 3 15-MAY-19 5FV2 1 REMARK REVDAT 2 23-MAR-16 5FV2 1 JRNL REVDAT 1 17-FEB-16 5FV2 0 JRNL AUTH A.WALKER,C.CHUNG,M.NEU,M.BURMAN,T.BATUWANGALA,G.JONES, JRNL AUTH 2 C.TANG,M.STEWARD,M.MULLIN,N.TOURNIER,A.LEWIS,J.KORCZYNSKA, JRNL AUTH 3 V.CHUNG,I.CATCHPOLE JRNL TITL NOVEL INTERACTION MECHANISM OF A DOMAIN ANTIBODY BASED JRNL TITL 2 INHIBITOR OF HUMAN VASCULAR ENDOTHELIAL GROWTH FACTOR WITH JRNL TITL 3 GREATER POTENCY THAN RANIBIZUMAB AND BEVACIZUMAB AND JRNL TITL 4 IMPROVED CAPACITY OVER AFLIBERCEPT. JRNL REF J.BIOL.CHEM. V. 291 5500 2016 JRNL REFN ISSN 0021-9258 JRNL PMID 26728464 JRNL DOI 10.1074/JBC.M115.691162 REMARK 2 REMARK 2 RESOLUTION. 3.45 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) : 3.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.62 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 13340 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) : 0.215 REMARK 3 R VALUE (WORKING SET) : 0.212 REMARK 3 FREE R VALUE : 0.263 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 706 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) : 3.45 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.54 REMARK 3 REFLECTION IN BIN (WORKING SET) : 990 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.81 REMARK 3 BIN R VALUE (WORKING SET) : 0.3330 REMARK 3 BIN FREE R VALUE SET COUNT : 54 REMARK 3 BIN FREE R VALUE : 0.3520 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5022 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 108.5 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.45000 REMARK 3 B22 (A**2) : -0.78000 REMARK 3 B33 (A**2) : -0.02000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.60000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.567 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.457 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 32.857 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.929 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.888 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5151 ; 0.004 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 4727 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6970 ; 0.789 ; 1.958 REMARK 3 BOND ANGLES OTHERS (DEGREES): 10940 ; 0.967 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 631 ; 4.566 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 232 ;29.588 ;23.966 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 878 ;12.580 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 30 ;17.170 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 736 ; 0.047 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5794 ; 0.003 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1170 ; 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): 2542 ; 2.259 ;14.519 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2541 ; 2.258 ;14.517 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3167 ; 4.047 ;32.642 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2609 ; 2.077 ;14.826 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 5FV2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 02-FEB-16. REMARK 100 THE DEPOSITION ID IS D_1290064984. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-JUN-09 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 : ESRF REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.93950 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14048 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.450 REMARK 200 RESOLUTION RANGE LOW (A) : 51.340 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : 0.01000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.64 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 0.44000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.700 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: NONE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 64.29 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.44 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRIS PH 8.5, 7%PEG6000, 0.2M REMARK 280 MGCL2 20C, 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 53.55400 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 65.19850 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 53.55400 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 65.19850 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6200 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21270 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -49.2 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, C, V, W 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 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6220 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21200 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -45.4 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, X 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 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 SER B 116 REMARK 465 ALA V 1 REMARK 465 PRO V 2 REMARK 465 MET V 3 REMARK 465 ALA V 4 REMARK 465 GLU V 5 REMARK 465 GLY V 6 REMARK 465 GLY V 7 REMARK 465 GLY V 8 REMARK 465 GLN V 9 REMARK 465 ASN V 10 REMARK 465 HIS V 11 REMARK 465 HIS V 12 REMARK 465 ASP V 109 REMARK 465 ARG V 110 REMARK 465 HIS V 111 REMARK 465 HIS V 112 REMARK 465 HIS V 113 REMARK 465 HIS V 114 REMARK 465 HIS V 115 REMARK 465 HIS V 116 REMARK 465 ALA W 1 REMARK 465 PRO W 2 REMARK 465 MET W 3 REMARK 465 ALA W 4 REMARK 465 GLU W 5 REMARK 465 GLY W 6 REMARK 465 GLY W 7 REMARK 465 GLY W 8 REMARK 465 GLN W 9 REMARK 465 ASN W 10 REMARK 465 HIS W 11 REMARK 465 ASP W 109 REMARK 465 ARG W 110 REMARK 465 HIS W 111 REMARK 465 HIS W 112 REMARK 465 HIS W 113 REMARK 465 HIS W 114 REMARK 465 HIS W 115 REMARK 465 HIS W 116 REMARK 465 ALA X 1 REMARK 465 PRO X 2 REMARK 465 MET X 3 REMARK 465 ALA X 4 REMARK 465 GLU X 5 REMARK 465 GLY X 6 REMARK 465 GLY X 7 REMARK 465 GLY X 8 REMARK 465 GLN X 9 REMARK 465 ASN X 10 REMARK 465 HIS X 11 REMARK 465 ASP X 109 REMARK 465 ARG X 110 REMARK 465 HIS X 111 REMARK 465 HIS X 112 REMARK 465 HIS X 113 REMARK 465 HIS X 114 REMARK 465 HIS X 115 REMARK 465 HIS X 116 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 102 CG CD CE NZ REMARK 470 LYS C 98 CG CD CE NZ REMARK 470 LYS W 84 CG CD CE NZ REMARK 470 LYS X 108 CG CD 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 NE2 GLN C 39 O LYS C 43 2.01 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 LYS A 76 CE LYS A 76 NZ -0.184 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 VAL A 48 -62.81 -100.93 REMARK 500 GLU V 42 48.74 -141.96 REMARK 500 GLN V 87 35.96 -143.11 REMARK 500 GLU W 42 59.54 -145.84 REMARK 500 GLU X 13 40.99 -103.21 REMARK 500 GLU X 42 43.64 -143.24 REMARK 500 GLN X 87 59.96 -146.85 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5FV1 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HVEGF IN COMPLEX WITH VK DOMAIN ANTIBODY REMARK 999 REMARK 999 SEQUENCE REMARK 999 RESIDUAL C-TERMINAL POLYHIS PURIFICATION TAG DBREF 5FV2 A 1 116 PDB 5FV2 5FV2 1 116 DBREF 5FV2 B 1 116 PDB 5FV2 5FV2 1 116 DBREF 5FV2 C 1 116 PDB 5FV2 5FV2 1 116 DBREF 5FV2 V 1 110 UNP P15692 VEGFA_HUMAN 27 136 DBREF 5FV2 W 1 110 UNP P15692 VEGFA_HUMAN 27 136 DBREF 5FV2 X 1 110 UNP P15692 VEGFA_HUMAN 27 136 SEQADV 5FV2 HIS V 111 UNP P15692 EXPRESSION TAG SEQADV 5FV2 HIS V 112 UNP P15692 EXPRESSION TAG SEQADV 5FV2 HIS V 113 UNP P15692 EXPRESSION TAG SEQADV 5FV2 HIS V 114 UNP P15692 EXPRESSION TAG SEQADV 5FV2 HIS V 115 UNP P15692 EXPRESSION TAG SEQADV 5FV2 HIS V 116 UNP P15692 EXPRESSION TAG SEQADV 5FV2 HIS W 111 UNP P15692 EXPRESSION TAG SEQADV 5FV2 HIS W 112 UNP P15692 EXPRESSION TAG SEQADV 5FV2 HIS W 113 UNP P15692 EXPRESSION TAG SEQADV 5FV2 HIS W 114 UNP P15692 EXPRESSION TAG SEQADV 5FV2 HIS W 115 UNP P15692 EXPRESSION TAG SEQADV 5FV2 HIS W 116 UNP P15692 EXPRESSION TAG SEQADV 5FV2 HIS X 111 UNP P15692 EXPRESSION TAG SEQADV 5FV2 HIS X 112 UNP P15692 EXPRESSION TAG SEQADV 5FV2 HIS X 113 UNP P15692 EXPRESSION TAG SEQADV 5FV2 HIS X 114 UNP P15692 EXPRESSION TAG SEQADV 5FV2 HIS X 115 UNP P15692 EXPRESSION TAG SEQADV 5FV2 HIS X 116 UNP P15692 EXPRESSION TAG SEQRES 1 A 116 GLU VAL GLN LEU LEU VAL SER GLY GLY GLY LEU VAL GLN SEQRES 2 A 116 PRO GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 A 116 PHE THR PHE LYS ALA TYR PRO MET MET TRP VAL ARG GLN SEQRES 4 A 116 ALA PRO GLY LYS GLY LEU GLU TRP VAL SER GLU ILE SER SEQRES 5 A 116 PRO SER GLY SER TYR THR TYR TYR ALA ASP SER VAL LYS SEQRES 6 A 116 GLY ARG PHE THR ILE SER ARG ASP ASN SER LYS ASN THR SEQRES 7 A 116 LEU TYR LEU GLN MET ASN SER LEU ARG ALA GLU ASP THR SEQRES 8 A 116 ALA VAL TYR TYR CYS ALA LYS ASP PRO ARG LYS LEU ASP SEQRES 9 A 116 TYR TRP GLY GLN GLY THR LEU VAL THR VAL SER SER SEQRES 1 B 116 GLU VAL GLN LEU LEU VAL SER GLY GLY GLY LEU VAL GLN SEQRES 2 B 116 PRO GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 B 116 PHE THR PHE LYS ALA TYR PRO MET MET TRP VAL ARG GLN SEQRES 4 B 116 ALA PRO GLY LYS GLY LEU GLU TRP VAL SER GLU ILE SER SEQRES 5 B 116 PRO SER GLY SER TYR THR TYR TYR ALA ASP SER VAL LYS SEQRES 6 B 116 GLY ARG PHE THR ILE SER ARG ASP ASN SER LYS ASN THR SEQRES 7 B 116 LEU TYR LEU GLN MET ASN SER LEU ARG ALA GLU ASP THR SEQRES 8 B 116 ALA VAL TYR TYR CYS ALA LYS ASP PRO ARG LYS LEU ASP SEQRES 9 B 116 TYR TRP GLY GLN GLY THR LEU VAL THR VAL SER SER SEQRES 1 C 116 GLU VAL GLN LEU LEU VAL SER GLY GLY GLY LEU VAL GLN SEQRES 2 C 116 PRO GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 C 116 PHE THR PHE LYS ALA TYR PRO MET MET TRP VAL ARG GLN SEQRES 4 C 116 ALA PRO GLY LYS GLY LEU GLU TRP VAL SER GLU ILE SER SEQRES 5 C 116 PRO SER GLY SER TYR THR TYR TYR ALA ASP SER VAL LYS SEQRES 6 C 116 GLY ARG PHE THR ILE SER ARG ASP ASN SER LYS ASN THR SEQRES 7 C 116 LEU TYR LEU GLN MET ASN SER LEU ARG ALA GLU ASP THR SEQRES 8 C 116 ALA VAL TYR TYR CYS ALA LYS ASP PRO ARG LYS LEU ASP SEQRES 9 C 116 TYR TRP GLY GLN GLY THR LEU VAL THR VAL SER SER SEQRES 1 V 116 ALA PRO MET ALA GLU GLY GLY GLY GLN ASN HIS HIS GLU SEQRES 2 V 116 VAL VAL LYS PHE MET ASP VAL TYR GLN ARG SER TYR CYS SEQRES 3 V 116 HIS PRO ILE GLU THR LEU VAL ASP ILE PHE GLN GLU TYR SEQRES 4 V 116 PRO ASP GLU ILE GLU TYR ILE PHE LYS PRO SER CYS VAL SEQRES 5 V 116 PRO LEU MET ARG CYS GLY GLY CYS CYS ASN ASP GLU GLY SEQRES 6 V 116 LEU GLU CYS VAL PRO THR GLU GLU SER ASN ILE THR MET SEQRES 7 V 116 GLN ILE MET ARG ILE LYS PRO HIS GLN GLY GLN HIS ILE SEQRES 8 V 116 GLY GLU MET SER PHE LEU GLN HIS ASN LYS CYS GLU CYS SEQRES 9 V 116 ARG PRO LYS LYS ASP ARG HIS HIS HIS HIS HIS HIS SEQRES 1 W 116 ALA PRO MET ALA GLU GLY GLY GLY GLN ASN HIS HIS GLU SEQRES 2 W 116 VAL VAL LYS PHE MET ASP VAL TYR GLN ARG SER TYR CYS SEQRES 3 W 116 HIS PRO ILE GLU THR LEU VAL ASP ILE PHE GLN GLU TYR SEQRES 4 W 116 PRO ASP GLU ILE GLU TYR ILE PHE LYS PRO SER CYS VAL SEQRES 5 W 116 PRO LEU MET ARG CYS GLY GLY CYS CYS ASN ASP GLU GLY SEQRES 6 W 116 LEU GLU CYS VAL PRO THR GLU GLU SER ASN ILE THR MET SEQRES 7 W 116 GLN ILE MET ARG ILE LYS PRO HIS GLN GLY GLN HIS ILE SEQRES 8 W 116 GLY GLU MET SER PHE LEU GLN HIS ASN LYS CYS GLU CYS SEQRES 9 W 116 ARG PRO LYS LYS ASP ARG HIS HIS HIS HIS HIS HIS SEQRES 1 X 116 ALA PRO MET ALA GLU GLY GLY GLY GLN ASN HIS HIS GLU SEQRES 2 X 116 VAL VAL LYS PHE MET ASP VAL TYR GLN ARG SER TYR CYS SEQRES 3 X 116 HIS PRO ILE GLU THR LEU VAL ASP ILE PHE GLN GLU TYR SEQRES 4 X 116 PRO ASP GLU ILE GLU TYR ILE PHE LYS PRO SER CYS VAL SEQRES 5 X 116 PRO LEU MET ARG CYS GLY GLY CYS CYS ASN ASP GLU GLY SEQRES 6 X 116 LEU GLU CYS VAL PRO THR GLU GLU SER ASN ILE THR MET SEQRES 7 X 116 GLN ILE MET ARG ILE LYS PRO HIS GLN GLY GLN HIS ILE SEQRES 8 X 116 GLY GLU MET SER PHE LEU GLN HIS ASN LYS CYS GLU CYS SEQRES 9 X 116 ARG PRO LYS LYS ASP ARG HIS HIS HIS HIS HIS HIS HELIX 1 1 ARG A 87 THR A 91 5 5 HELIX 2 2 THR B 28 TYR B 32 5 5 HELIX 3 3 ARG B 87 THR B 91 5 5 HELIX 4 4 ARG C 87 THR C 91 5 5 HELIX 5 5 LYS V 16 SER V 24 1 9 HELIX 6 6 ILE V 35 TYR V 39 1 5 HELIX 7 7 LYS W 16 TYR W 25 1 10 HELIX 8 8 ILE W 35 TYR W 39 1 5 HELIX 9 9 LYS X 16 TYR X 25 1 10 HELIX 10 10 ILE X 35 TYR X 39 1 5 SHEET 1 AA 4 GLN A 3 SER A 7 0 SHEET 2 AA 4 SER A 17 SER A 25 -1 O SER A 21 N SER A 7 SHEET 3 AA 4 THR A 78 ASN A 84 -1 O LEU A 79 N CYS A 22 SHEET 4 AA 4 THR A 69 ASP A 73 -1 O THR A 69 N GLN A 82 SHEET 1 AB 6 LEU A 11 VAL A 12 0 SHEET 2 AB 6 GLY A 109 VAL A 114 1 O THR A 113 N VAL A 12 SHEET 3 AB 6 ALA A 92 ALA A 97 -1 O ALA A 92 N VAL A 112 SHEET 4 AB 6 MET A 34 GLN A 39 -1 O MET A 35 N ALA A 97 SHEET 5 AB 6 LEU A 45 ILE A 51 -1 O GLU A 46 N ARG A 38 SHEET 6 AB 6 THR A 58 TYR A 60 -1 O TYR A 59 N GLU A 50 SHEET 1 BA 4 GLN B 3 SER B 7 0 SHEET 2 BA 4 SER B 17 SER B 25 -1 O SER B 21 N SER B 7 SHEET 3 BA 4 THR B 78 ASN B 84 -1 O LEU B 79 N CYS B 22 SHEET 4 BA 4 THR B 69 ASP B 73 -1 O THR B 69 N GLN B 82 SHEET 1 BB 6 LEU B 11 VAL B 12 0 SHEET 2 BB 6 GLY B 109 VAL B 114 1 O THR B 113 N VAL B 12 SHEET 3 BB 6 ALA B 92 ALA B 97 -1 O ALA B 92 N VAL B 112 SHEET 4 BB 6 MET B 34 GLN B 39 -1 O MET B 35 N ALA B 97 SHEET 5 BB 6 LEU B 45 ILE B 51 -1 O GLU B 46 N ARG B 38 SHEET 6 BB 6 THR B 58 TYR B 60 -1 O TYR B 59 N GLU B 50 SHEET 1 CA 4 GLN C 3 SER C 7 0 SHEET 2 CA 4 SER C 17 SER C 25 -1 O SER C 21 N SER C 7 SHEET 3 CA 4 THR C 78 ASN C 84 -1 O LEU C 79 N CYS C 22 SHEET 4 CA 4 THR C 69 ASP C 73 -1 O THR C 69 N GLN C 82 SHEET 1 CB 6 GLY C 10 VAL C 12 0 SHEET 2 CB 6 THR C 110 VAL C 114 1 O LEU C 111 N GLY C 10 SHEET 3 CB 6 ALA C 92 ALA C 97 -1 O ALA C 92 N VAL C 112 SHEET 4 CB 6 MET C 34 GLN C 39 -1 O MET C 35 N ALA C 97 SHEET 5 CB 6 LEU C 45 ILE C 51 -1 O GLU C 46 N ARG C 38 SHEET 6 CB 6 THR C 58 TYR C 60 -1 O TYR C 59 N GLU C 50 SHEET 1 VA 2 HIS V 27 ASP V 34 0 SHEET 2 VA 2 CYS V 51 GLY V 58 -1 O VAL V 52 N VAL V 33 SHEET 1 VB 2 ILE V 46 LYS V 48 0 SHEET 2 VB 2 LEU V 66 ILE V 83 -1 O MET V 81 N LYS V 48 SHEET 1 VC 2 GLN V 89 PRO V 106 0 SHEET 2 VC 2 LEU V 66 ILE V 83 -1 O GLU V 67 N ARG V 105 SHEET 1 WA 2 VAL W 14 VAL W 15 0 SHEET 2 WA 2 LEU V 66 ILE V 83 1 O THR V 77 N VAL W 15 SHEET 1 WB 2 HIS W 27 ASP W 34 0 SHEET 2 WB 2 CYS W 51 GLY W 58 -1 O VAL W 52 N VAL W 33 SHEET 1 WC 3 ILE W 46 LYS W 48 0 SHEET 2 WC 3 LEU W 66 ILE W 83 -1 O MET W 81 N LYS W 48 SHEET 3 WC 3 GLN W 89 PRO W 106 -1 O HIS W 90 N ARG W 82 SHEET 1 XA 2 HIS X 27 ASP X 34 0 SHEET 2 XA 2 CYS X 51 GLY X 58 -1 O VAL X 52 N VAL X 33 SHEET 1 XB 3 ILE X 46 LYS X 48 0 SHEET 2 XB 3 LEU X 66 ILE X 83 -1 O MET X 81 N LYS X 48 SHEET 3 XB 3 GLN X 89 PRO X 106 -1 O HIS X 90 N ARG X 82 SSBOND 1 CYS A 22 CYS A 96 1555 1555 2.04 SSBOND 2 CYS B 22 CYS B 96 1555 1555 2.04 SSBOND 3 CYS C 22 CYS C 96 1555 1555 2.04 SSBOND 4 CYS V 26 CYS V 68 1555 1555 2.03 SSBOND 5 CYS V 51 CYS W 60 1555 1555 2.04 SSBOND 6 CYS V 57 CYS V 102 1555 1555 2.04 SSBOND 7 CYS V 60 CYS W 51 1555 1555 2.04 SSBOND 8 CYS V 61 CYS V 104 1555 1555 2.03 SSBOND 9 CYS W 26 CYS W 68 1555 1555 2.03 SSBOND 10 CYS W 57 CYS W 102 1555 1555 2.04 SSBOND 11 CYS W 61 CYS W 104 1555 1555 2.03 SSBOND 12 CYS X 26 CYS X 68 1555 1555 2.03 SSBOND 13 CYS X 57 CYS X 102 1555 1555 2.04 SSBOND 14 CYS X 61 CYS X 104 1555 1555 2.04 CISPEP 1 LYS V 48 PRO V 49 0 -3.70 CISPEP 2 LYS W 48 PRO W 49 0 -2.01 CISPEP 3 LYS X 48 PRO X 49 0 -4.90 CRYST1 107.108 130.397 81.178 90.00 106.53 90.00 C 1 2 1 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 0.009336 0.000000 0.002771 0.00000 SCALE2 0.000000 0.007669 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012850 0.00000