HEADER SIGNALING PROTEIN/IMMUNE SYSTEM 21-APR-15 4ZFF TITLE DUAL-ACTING FAB 5A12 IN COMPLEX WITH VEGF COMPND MOL_ID: 1; COMPND 2 MOLECULE: FRAGMENT ANTIGEN BINDING (FAB) 5A12 HEAVY CHAIN; COMPND 3 CHAIN: A, H; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: FRAGMENT ANTIGEN BINDING (FAB) 5A12 LIGHT CHAIN; COMPND 7 CHAIN: B, L; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: VASCULAR ENDOTHELIAL GROWTH FACTOR A; COMPND 11 CHAIN: C, D; COMPND 12 FRAGMENT: UNP RESIDUES 217-315; COMPND 13 SYNONYM: VEGF-A,VASCULAR PERMEABILITY FACTOR,VPF; COMPND 14 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; SOURCE 13 MOL_ID: 3; SOURCE 14 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 15 ORGANISM_COMMON: HUMAN; SOURCE 16 ORGANISM_TAXID: 9606; SOURCE 17 GENE: VEGFA, VEGF; SOURCE 18 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 19 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS FAB, DAF, ANGIOGENESIS, TIE RECEPTOR, SIGNALING PROTEIN-IMMUNE SYSTEM KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR S.F.HARRIS,P.WU REVDAT 2 16-SEP-15 4ZFF 1 JRNL REVDAT 1 01-JUL-15 4ZFF 0 JRNL AUTH P.KOENIG,C.V.LEE,S.SANOWAR,P.WU,J.STINSON,S.F.HARRIS,G.FUH JRNL TITL DEEP SEQUENCING-GUIDED DESIGN OF A HIGH AFFINITY DUAL JRNL TITL 2 SPECIFICITY ANTIBODY TO TARGET TWO ANGIOGENIC FACTORS IN JRNL TITL 3 NEOVASCULAR AGE-RELATED MACULAR DEGENERATION. JRNL REF J.BIOL.CHEM. V. 290 21773 2015 JRNL REFN ESSN 1083-351X JRNL PMID 26088137 JRNL DOI 10.1074/JBC.M115.662783 REMARK 2 REMARK 2 RESOLUTION. 2.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.11.5 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.95 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 37690 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) : 0.199 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.238 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.130 REMARK 3 FREE R VALUE TEST SET COUNT : 1933 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 19 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 2.75 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.83 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.94 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 2887 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2388 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2726 REMARK 3 BIN R VALUE (WORKING SET) : 0.2335 REMARK 3 BIN FREE R VALUE : 0.3289 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.58 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 161 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 7928 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 429 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 65.29 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 68.61 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.61970 REMARK 3 B22 (A**2) : 7.75240 REMARK 3 B33 (A**2) : -8.37200 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.343 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 1.085 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.311 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.765 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.307 REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.924 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.901 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 8136 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 11055 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 2688 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 171 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 1185 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 8136 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : NULL ; NULL ; NULL REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 1069 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 9014 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.17 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 3.23 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 20.36 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4ZFF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-APR-15. REMARK 100 THE DEPOSITION ID IS D_1000209160. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-NOV-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-G REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97856 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 38026 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.750 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 6.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.4920 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.20 REMARK 200 R MERGE FOR SHELL (I) : 0.58400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.49 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.96 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS PH 8.0, 2.0 M AMMONIUM REMARK 280 SULFATE, 0.3 M NDSB-195, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 43.70300 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 156.94600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 43.70300 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 156.94600 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: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 13630 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 46060 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -108.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, H, L 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 SER A 127 REMARK 465 SER A 128 REMARK 465 LYS A 129 REMARK 465 SER A 130 REMARK 465 THR A 131 REMARK 465 SER A 132 REMARK 465 GLY A 133 REMARK 465 GLY A 134 REMARK 465 TRP A 154 REMARK 465 ASN A 155 REMARK 465 LYS A 210 REMARK 465 VAL A 211 REMARK 465 GLU A 212 REMARK 465 PRO A 213 REMARK 465 LYS A 214 REMARK 465 SER A 215 REMARK 465 CYS A 216 REMARK 465 ASP A 217 REMARK 465 LYS A 218 REMARK 465 THR A 219 REMARK 465 HIS A 220 REMARK 465 THR A 221 REMARK 465 ALA B 153 REMARK 465 LEU B 154 REMARK 465 GLN B 155 REMARK 465 GLU B 213 REMARK 465 CYS B 214 REMARK 465 HIS C 11 REMARK 465 HIS C 12 REMARK 465 ASP C 109 REMARK 465 SER H 127 REMARK 465 SER H 128 REMARK 465 LYS H 129 REMARK 465 SER H 130 REMARK 465 THR H 131 REMARK 465 SER H 132 REMARK 465 GLY H 133 REMARK 465 GLY H 134 REMARK 465 PRO H 213 REMARK 465 LYS H 214 REMARK 465 SER H 215 REMARK 465 CYS H 216 REMARK 465 ASP H 217 REMARK 465 LYS H 218 REMARK 465 THR H 219 REMARK 465 HIS H 220 REMARK 465 THR H 221 REMARK 465 GLU L 213 REMARK 465 CYS L 214 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 C 108 CG CD CE NZ REMARK 470 LYS D 108 CG CD CE NZ REMARK 470 ASP D 109 CG OD1 OD2 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 144 85.33 46.54 REMARK 500 THR A 160 -68.01 -137.46 REMARK 500 SER B 12 119.74 -162.24 REMARK 500 SER B 30 70.47 -69.78 REMARK 500 PHE B 31 -9.18 -160.76 REMARK 500 LEU B 47 -61.95 -104.36 REMARK 500 ALA B 51 -38.73 65.11 REMARK 500 ALA B 84 174.87 179.45 REMARK 500 LEU B 92 -60.98 -95.19 REMARK 500 ASN B 138 88.30 50.23 REMARK 500 ASN B 158 18.00 54.98 REMARK 500 ARG B 211 137.83 94.35 REMARK 500 CYS C 26 116.66 -24.52 REMARK 500 GLN C 87 -52.40 -120.25 REMARK 500 CYS D 26 116.34 -11.81 REMARK 500 ASN D 62 45.62 -107.17 REMARK 500 ASP H 144 85.43 47.37 REMARK 500 THR H 160 -43.36 -131.72 REMARK 500 LEU L 47 -61.54 -109.56 REMARK 500 ALA L 51 -39.13 65.42 REMARK 500 ALA L 84 174.99 179.81 REMARK 500 LEU L 92 -61.63 -95.03 REMARK 500 ASN L 138 74.01 46.47 REMARK 500 ARG L 211 131.92 96.76 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH H 433 DISTANCE = 5.82 ANGSTROMS REMARK 525 HOH H 434 DISTANCE = 6.17 ANGSTROMS REMARK 525 HOH H 435 DISTANCE = 6.39 ANGSTROMS REMARK 525 HOH H 436 DISTANCE = 6.75 ANGSTROMS REMARK 525 HOH H 437 DISTANCE = 7.19 ANGSTROMS REMARK 525 HOH H 438 DISTANCE = 9.34 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 L 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4ZFG RELATED DB: PDB DBREF 4ZFF A 1 221 PDB 4ZFF 4ZFF 1 221 DBREF 4ZFF B 1 214 PDB 4ZFF 4ZFF 1 214 DBREF 4ZFF C 11 109 UNP P15692 VEGFA_HUMAN 217 315 DBREF 4ZFF D 11 109 UNP P15692 VEGFA_HUMAN 217 315 DBREF 4ZFF H 1 221 PDB 4ZFF 4ZFF 1 221 DBREF 4ZFF L 1 214 PDB 4ZFF 4ZFF 1 214 SEQRES 1 A 228 GLU VAL GLN LEU VAL GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 A 228 PRO GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 A 228 PHE THR ILE SER ASP TYR TRP ILE HIS TRP VAL ARG GLN SEQRES 4 A 228 ALA PRO GLY LYS GLY LEU GLU TRP VAL ALA GLY ILE THR SEQRES 5 A 228 PRO ALA GLY GLY TYR THR TYR TYR ALA ASP SER VAL LYS SEQRES 6 A 228 GLY ARG PHE THR ILE SER ALA ASP THR SER LYS ASN THR SEQRES 7 A 228 ALA TYR LEU GLN MET ASN SER LEU ARG ALA GLU ASP THR SEQRES 8 A 228 ALA VAL TYR TYR CYS ALA ARG PHE VAL PHE PHE LEU PRO SEQRES 9 A 228 TYR ALA MET ASP TYR TRP GLY GLN GLY THR LEU VAL THR SEQRES 10 A 228 VAL SER SER ALA SER THR LYS GLY PRO SER VAL PHE PRO SEQRES 11 A 228 LEU ALA PRO SER SER LYS SER THR SER GLY GLY THR ALA SEQRES 12 A 228 ALA LEU GLY CYS LEU VAL LYS ASP TYR PHE PRO GLU PRO SEQRES 13 A 228 VAL THR VAL SER TRP ASN SER GLY ALA LEU THR SER GLY SEQRES 14 A 228 VAL HIS THR PHE PRO ALA VAL LEU GLN SER SER GLY LEU SEQRES 15 A 228 TYR SER LEU SER SER VAL VAL THR VAL PRO SER SER SER SEQRES 16 A 228 LEU GLY THR GLN THR TYR ILE CYS ASN VAL ASN HIS LYS SEQRES 17 A 228 PRO SER ASN THR LYS VAL ASP LYS LYS VAL GLU PRO LYS SEQRES 18 A 228 SER CYS ASP LYS THR HIS THR SEQRES 1 B 215 ASP ILE GLN MET THR GLN SER PRO SER SER LEU SER ALA SEQRES 2 B 215 SER VAL GLY ASP ARG VAL THR ILE THR CYS ARG ALA SER SEQRES 3 B 215 GLN PHE LEU SER SER PHE GLY VAL ALA TRP TYR GLN GLN SEQRES 4 B 215 LYS PRO GLY LYS ALA PRO LYS LEU LEU ILE TYR GLY ALA SEQRES 5 B 215 SER SER LEU TYR SER GLY VAL PRO SER ARG PHE SER GLY SEQRES 6 B 215 SER GLY SER GLY THR ASP PHE THR LEU THR ILE SER SER SEQRES 7 B 215 LEU GLN PRO GLU ASP PHE ALA THR TYR TYR CYS GLN GLN SEQRES 8 B 215 GLY LEU LEU SER PRO LEU THR PHE GLY GLN GLY THR LYS SEQRES 9 B 215 VAL GLU ILE LYS ARG THR VAL ALA ALA PRO SER VAL PHE SEQRES 10 B 215 ILE PHE PRO PRO SER ASP GLU GLN LEU LYS SER GLY THR SEQRES 11 B 215 ALA SER VAL VAL CYS LEU LEU ASN ASN PHE TYR PRO ARG SEQRES 12 B 215 GLU ALA LYS VAL GLN TRP LYS VAL ASP ASN ALA LEU GLN SEQRES 13 B 215 SER GLY ASN SER GLN GLU SER VAL THR GLU GLN ASP SER SEQRES 14 B 215 LYS ASP SER THR TYR SER LEU SER SER THR LEU THR LEU SEQRES 15 B 215 SER LYS ALA ASP TYR GLU LYS HIS LYS VAL TYR ALA CYS SEQRES 16 B 215 GLU VAL THR HIS GLN GLY LEU SER SER PRO VAL THR LYS SEQRES 17 B 215 SER PHE ASN ARG GLY GLU CYS SEQRES 1 C 99 HIS HIS GLU VAL VAL LYS PHE MET ASP VAL TYR GLN ARG SEQRES 2 C 99 SER TYR CYS HIS PRO ILE GLU THR LEU VAL ASP ILE PHE SEQRES 3 C 99 GLN GLU TYR PRO ASP GLU ILE GLU TYR ILE PHE LYS PRO SEQRES 4 C 99 SER CYS VAL PRO LEU MET ARG CYS GLY GLY CYS CYS ASN SEQRES 5 C 99 ASP GLU GLY LEU GLU CYS VAL PRO THR GLU GLU SER ASN SEQRES 6 C 99 ILE THR MET GLN ILE MET ARG ILE LYS PRO HIS GLN GLY SEQRES 7 C 99 GLN HIS ILE GLY GLU MET SER PHE LEU GLN HIS ASN LYS SEQRES 8 C 99 CYS GLU CYS ARG PRO LYS LYS ASP SEQRES 1 D 99 HIS HIS GLU VAL VAL LYS PHE MET ASP VAL TYR GLN ARG SEQRES 2 D 99 SER TYR CYS HIS PRO ILE GLU THR LEU VAL ASP ILE PHE SEQRES 3 D 99 GLN GLU TYR PRO ASP GLU ILE GLU TYR ILE PHE LYS PRO SEQRES 4 D 99 SER CYS VAL PRO LEU MET ARG CYS GLY GLY CYS CYS ASN SEQRES 5 D 99 ASP GLU GLY LEU GLU CYS VAL PRO THR GLU GLU SER ASN SEQRES 6 D 99 ILE THR MET GLN ILE MET ARG ILE LYS PRO HIS GLN GLY SEQRES 7 D 99 GLN HIS ILE GLY GLU MET SER PHE LEU GLN HIS ASN LYS SEQRES 8 D 99 CYS GLU CYS ARG PRO LYS LYS ASP SEQRES 1 H 228 GLU VAL GLN LEU VAL GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 H 228 PRO GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 H 228 PHE THR ILE SER ASP TYR TRP ILE HIS TRP VAL ARG GLN SEQRES 4 H 228 ALA PRO GLY LYS GLY LEU GLU TRP VAL ALA GLY ILE THR SEQRES 5 H 228 PRO ALA GLY GLY TYR THR TYR TYR ALA ASP SER VAL LYS SEQRES 6 H 228 GLY ARG PHE THR ILE SER ALA ASP THR SER LYS ASN THR SEQRES 7 H 228 ALA TYR LEU GLN MET ASN SER LEU ARG ALA GLU ASP THR SEQRES 8 H 228 ALA VAL TYR TYR CYS ALA ARG PHE VAL PHE PHE LEU PRO SEQRES 9 H 228 TYR ALA MET ASP TYR TRP GLY GLN GLY THR LEU VAL THR SEQRES 10 H 228 VAL SER SER ALA SER THR LYS GLY PRO SER VAL PHE PRO SEQRES 11 H 228 LEU ALA PRO SER SER LYS SER THR SER GLY GLY THR ALA SEQRES 12 H 228 ALA LEU GLY CYS LEU VAL LYS ASP TYR PHE PRO GLU PRO SEQRES 13 H 228 VAL THR VAL SER TRP ASN SER GLY ALA LEU THR SER GLY SEQRES 14 H 228 VAL HIS THR PHE PRO ALA VAL LEU GLN SER SER GLY LEU SEQRES 15 H 228 TYR SER LEU SER SER VAL VAL THR VAL PRO SER SER SER SEQRES 16 H 228 LEU GLY THR GLN THR TYR ILE CYS ASN VAL ASN HIS LYS SEQRES 17 H 228 PRO SER ASN THR LYS VAL ASP LYS LYS VAL GLU PRO LYS SEQRES 18 H 228 SER CYS ASP LYS THR HIS THR SEQRES 1 L 215 ASP ILE GLN MET THR GLN SER PRO SER SER LEU SER ALA SEQRES 2 L 215 SER VAL GLY ASP ARG VAL THR ILE THR CYS ARG ALA SER SEQRES 3 L 215 GLN PHE LEU SER SER PHE GLY VAL ALA TRP TYR GLN GLN SEQRES 4 L 215 LYS PRO GLY LYS ALA PRO LYS LEU LEU ILE TYR GLY ALA SEQRES 5 L 215 SER SER LEU TYR SER GLY VAL PRO SER ARG PHE SER GLY SEQRES 6 L 215 SER GLY SER GLY THR ASP PHE THR LEU THR ILE SER SER SEQRES 7 L 215 LEU GLN PRO GLU ASP PHE ALA THR TYR TYR CYS GLN GLN SEQRES 8 L 215 GLY LEU LEU SER PRO LEU THR PHE GLY GLN GLY THR LYS SEQRES 9 L 215 VAL GLU ILE LYS ARG THR VAL ALA ALA PRO SER VAL PHE SEQRES 10 L 215 ILE PHE PRO PRO SER ASP GLU GLN LEU LYS SER GLY THR SEQRES 11 L 215 ALA SER VAL VAL CYS LEU LEU ASN ASN PHE TYR PRO ARG SEQRES 12 L 215 GLU ALA LYS VAL GLN TRP LYS VAL ASP ASN ALA LEU GLN SEQRES 13 L 215 SER GLY ASN SER GLN GLU SER VAL THR GLU GLN ASP SER SEQRES 14 L 215 LYS ASP SER THR TYR SER LEU SER SER THR LEU THR LEU SEQRES 15 L 215 SER LYS ALA ASP TYR GLU LYS HIS LYS VAL TYR ALA CYS SEQRES 16 L 215 GLU VAL THR HIS GLN GLY LEU SER SER PRO VAL THR LYS SEQRES 17 L 215 SER PHE ASN ARG GLY GLU CYS HET SO4 L 301 5 HETNAM SO4 SULFATE ION FORMUL 7 SO4 O4 S 2- FORMUL 8 HOH *429(H2 O) HELIX 1 AA1 THR A 28 TYR A 32 5 5 HELIX 2 AA2 ARG A 83 THR A 87 5 5 HELIX 3 AA3 SER A 187 GLN A 192 1 6 HELIX 4 AA4 HIS A 200 ASN A 204 5 5 HELIX 5 AA5 GLN B 79 PHE B 83 5 5 HELIX 6 AA6 SER B 121 SER B 127 1 7 HELIX 7 AA7 LYS B 183 LYS B 188 1 6 HELIX 8 AA8 LYS C 16 TYR C 25 1 10 HELIX 9 AA9 ILE C 35 TYR C 39 1 5 HELIX 10 AB1 LYS D 16 TYR D 25 1 10 HELIX 11 AB2 ILE D 35 TYR D 39 1 5 HELIX 12 AB3 THR H 28 TYR H 32 5 5 HELIX 13 AB4 ARG H 83 THR H 87 5 5 HELIX 14 AB5 SER H 187 GLN H 192 1 6 HELIX 15 AB6 HIS H 200 ASN H 204 5 5 HELIX 16 AB7 SER L 29 PHE L 31 5 3 HELIX 17 AB8 GLN L 79 PHE L 83 5 5 HELIX 18 AB9 SER L 121 SER L 127 1 7 HELIX 19 AC1 LYS L 183 LYS L 188 1 6 SHEET 1 AA1 4 GLN A 3 SER A 7 0 SHEET 2 AA1 4 LEU A 18 SER A 25 -1 O ALA A 23 N VAL A 5 SHEET 3 AA1 4 THR A 77 MET A 82 -1 O MET A 82 N LEU A 18 SHEET 4 AA1 4 PHE A 67 ASP A 72 -1 N ASP A 72 O THR A 77 SHEET 1 AA2 6 GLY A 10 VAL A 12 0 SHEET 2 AA2 6 THR A 107 VAL A 111 1 O THR A 110 N VAL A 12 SHEET 3 AA2 6 ALA A 88 VAL A 96 -1 N TYR A 90 O THR A 107 SHEET 4 AA2 6 TRP A 33 GLN A 39 -1 N VAL A 37 O TYR A 91 SHEET 5 AA2 6 LEU A 45 ILE A 51 -1 O GLU A 46 N ARG A 38 SHEET 6 AA2 6 THR A 57 TYR A 59 -1 O TYR A 58 N GLY A 50 SHEET 1 AA3 4 GLY A 10 VAL A 12 0 SHEET 2 AA3 4 THR A 107 VAL A 111 1 O THR A 110 N VAL A 12 SHEET 3 AA3 4 ALA A 88 VAL A 96 -1 N TYR A 90 O THR A 107 SHEET 4 AA3 4 ALA A 100B TRP A 103 -1 O TYR A 102 N ARG A 94 SHEET 1 AA4 4 SER A 120 LEU A 124 0 SHEET 2 AA4 4 ALA A 136 TYR A 145 -1 O LEU A 141 N PHE A 122 SHEET 3 AA4 4 TYR A 176 VAL A 184 -1 O LEU A 178 N VAL A 142 SHEET 4 AA4 4 VAL A 163 THR A 165 -1 N HIS A 164 O VAL A 181 SHEET 1 AA5 4 SER A 120 LEU A 124 0 SHEET 2 AA5 4 ALA A 136 TYR A 145 -1 O LEU A 141 N PHE A 122 SHEET 3 AA5 4 TYR A 176 VAL A 184 -1 O LEU A 178 N VAL A 142 SHEET 4 AA5 4 VAL A 169 LEU A 170 -1 N VAL A 169 O SER A 177 SHEET 1 AA6 2 THR A 151 VAL A 152 0 SHEET 2 AA6 2 VAL A 198 ASN A 199 -1 O ASN A 199 N THR A 151 SHEET 1 AA7 3 MET B 4 SER B 7 0 SHEET 2 AA7 3 VAL B 19 LEU B 28 -1 O ARG B 24 N THR B 5 SHEET 3 AA7 3 PHE B 62 ILE B 75 -1 O PHE B 71 N CYS B 23 SHEET 1 AA8 6 SER B 10 SER B 14 0 SHEET 2 AA8 6 THR B 102 LYS B 107 1 O LYS B 103 N LEU B 11 SHEET 3 AA8 6 ALA B 84 GLN B 90 -1 N ALA B 84 O VAL B 104 SHEET 4 AA8 6 VAL B 33 GLN B 38 -1 N TYR B 36 O TYR B 87 SHEET 5 AA8 6 LYS B 45 TYR B 49 -1 O LYS B 45 N GLN B 37 SHEET 6 AA8 6 SER B 53 LEU B 54 -1 O SER B 53 N TYR B 49 SHEET 1 AA9 4 SER B 10 SER B 14 0 SHEET 2 AA9 4 THR B 102 LYS B 107 1 O LYS B 103 N LEU B 11 SHEET 3 AA9 4 ALA B 84 GLN B 90 -1 N ALA B 84 O VAL B 104 SHEET 4 AA9 4 THR B 97 PHE B 98 -1 O THR B 97 N GLN B 90 SHEET 1 AB1 4 SER B 114 PHE B 118 0 SHEET 2 AB1 4 THR B 129 PHE B 139 -1 O ASN B 137 N SER B 114 SHEET 3 AB1 4 TYR B 173 SER B 182 -1 O LEU B 181 N ALA B 130 SHEET 4 AB1 4 GLN B 160 VAL B 163 -1 N SER B 162 O SER B 176 SHEET 1 AB2 3 LYS B 145 VAL B 150 0 SHEET 2 AB2 3 TYR B 192 THR B 197 -1 O GLU B 195 N GLN B 147 SHEET 3 AB2 3 VAL B 205 PHE B 209 -1 O VAL B 205 N VAL B 196 SHEET 1 AB3 2 HIS C 27 ASP C 34 0 SHEET 2 AB3 2 CYS C 51 GLY C 58 -1 O ARG C 56 N ILE C 29 SHEET 1 AB4 3 ILE C 46 LYS C 48 0 SHEET 2 AB4 3 LEU C 66 LYS C 84 -1 O MET C 81 N LYS C 48 SHEET 3 AB4 3 GLY C 88 PRO C 106 -1 O HIS C 90 N ARG C 82 SHEET 1 AB5 2 HIS D 27 ASP D 34 0 SHEET 2 AB5 2 CYS D 51 GLY D 58 -1 O ARG D 56 N ILE D 29 SHEET 1 AB6 3 ILE D 46 LYS D 48 0 SHEET 2 AB6 3 LEU D 66 LYS D 84 -1 O MET D 81 N LYS D 48 SHEET 3 AB6 3 GLY D 88 PRO D 106 -1 O HIS D 90 N ARG D 82 SHEET 1 AB7 4 GLN H 3 SER H 7 0 SHEET 2 AB7 4 LEU H 18 SER H 25 -1 O ALA H 23 N VAL H 5 SHEET 3 AB7 4 THR H 77 MET H 82 -1 O MET H 82 N LEU H 18 SHEET 4 AB7 4 PHE H 67 ASP H 72 -1 N THR H 68 O GLN H 81 SHEET 1 AB8 6 GLY H 10 VAL H 12 0 SHEET 2 AB8 6 THR H 107 VAL H 111 1 O THR H 110 N VAL H 12 SHEET 3 AB8 6 ALA H 88 VAL H 96 -1 N TYR H 90 O THR H 107 SHEET 4 AB8 6 TRP H 33 GLN H 39 -1 N VAL H 37 O TYR H 91 SHEET 5 AB8 6 LEU H 45 ILE H 51 -1 O GLU H 46 N ARG H 38 SHEET 6 AB8 6 THR H 57 TYR H 59 -1 O TYR H 58 N GLY H 50 SHEET 1 AB9 4 GLY H 10 VAL H 12 0 SHEET 2 AB9 4 THR H 107 VAL H 111 1 O THR H 110 N VAL H 12 SHEET 3 AB9 4 ALA H 88 VAL H 96 -1 N TYR H 90 O THR H 107 SHEET 4 AB9 4 ALA H 100B TRP H 103 -1 O TYR H 102 N ARG H 94 SHEET 1 AC1 4 SER H 120 LEU H 124 0 SHEET 2 AC1 4 ALA H 136 TYR H 145 -1 O LEU H 141 N PHE H 122 SHEET 3 AC1 4 TYR H 176 VAL H 184 -1 O VAL H 184 N ALA H 136 SHEET 4 AC1 4 HIS H 164 THR H 165 -1 N HIS H 164 O VAL H 181 SHEET 1 AC2 4 SER H 120 LEU H 124 0 SHEET 2 AC2 4 ALA H 136 TYR H 145 -1 O LEU H 141 N PHE H 122 SHEET 3 AC2 4 TYR H 176 VAL H 184 -1 O VAL H 184 N ALA H 136 SHEET 4 AC2 4 VAL H 169 LEU H 170 -1 N VAL H 169 O SER H 177 SHEET 1 AC3 3 THR H 151 TRP H 154 0 SHEET 2 AC3 3 TYR H 194 ASN H 199 -1 O ASN H 197 N SER H 153 SHEET 3 AC3 3 ASP H 208 VAL H 211 -1 O VAL H 211 N TYR H 194 SHEET 1 AC4 3 MET L 4 SER L 7 0 SHEET 2 AC4 3 VAL L 19 LEU L 28 -1 O ARG L 24 N THR L 5 SHEET 3 AC4 3 PHE L 62 ILE L 75 -1 O PHE L 71 N CYS L 23 SHEET 1 AC5 6 SER L 10 ALA L 13 0 SHEET 2 AC5 6 THR L 102 ILE L 106 1 O LYS L 103 N LEU L 11 SHEET 3 AC5 6 ALA L 84 GLN L 90 -1 N ALA L 84 O VAL L 104 SHEET 4 AC5 6 VAL L 33 GLN L 38 -1 N TYR L 36 O TYR L 87 SHEET 5 AC5 6 LYS L 45 TYR L 49 -1 O LYS L 45 N GLN L 37 SHEET 6 AC5 6 SER L 53 LEU L 54 -1 O SER L 53 N TYR L 49 SHEET 1 AC6 4 SER L 10 ALA L 13 0 SHEET 2 AC6 4 THR L 102 ILE L 106 1 O LYS L 103 N LEU L 11 SHEET 3 AC6 4 ALA L 84 GLN L 90 -1 N ALA L 84 O VAL L 104 SHEET 4 AC6 4 THR L 97 PHE L 98 -1 O THR L 97 N GLN L 90 SHEET 1 AC7 4 SER L 114 PHE L 118 0 SHEET 2 AC7 4 THR L 129 PHE L 139 -1 O ASN L 137 N SER L 114 SHEET 3 AC7 4 TYR L 173 SER L 182 -1 O LEU L 179 N VAL L 132 SHEET 4 AC7 4 SER L 159 VAL L 163 -1 N GLN L 160 O THR L 178 SHEET 1 AC8 4 ALA L 153 LEU L 154 0 SHEET 2 AC8 4 LYS L 145 VAL L 150 -1 N VAL L 150 O ALA L 153 SHEET 3 AC8 4 TYR L 192 THR L 197 -1 O GLU L 195 N GLN L 147 SHEET 4 AC8 4 VAL L 205 PHE L 209 -1 O VAL L 205 N VAL L 196 SSBOND 1 CYS A 22 CYS A 92 1555 1555 2.72 SSBOND 2 CYS B 23 CYS B 88 1555 1555 2.63 SSBOND 3 CYS C 26 CYS C 68 1555 1555 2.44 SSBOND 4 CYS C 51 CYS D 60 1555 1555 2.97 SSBOND 5 CYS C 57 CYS C 102 1555 1555 2.42 SSBOND 6 CYS C 60 CYS D 51 1555 1555 2.73 SSBOND 7 CYS C 61 CYS C 104 1555 1555 2.59 SSBOND 8 CYS D 26 CYS D 68 1555 1555 2.44 SSBOND 9 CYS D 57 CYS D 102 1555 1555 2.45 SSBOND 10 CYS D 61 CYS D 104 1555 1555 2.57 SSBOND 11 CYS H 22 CYS H 92 1555 1555 2.71 SSBOND 12 CYS H 140 CYS H 196 1555 1555 2.58 SSBOND 13 CYS L 23 CYS L 88 1555 1555 2.56 SSBOND 14 CYS L 134 CYS L 194 1555 1555 2.11 CISPEP 1 PHE A 146 PRO A 147 0 -6.68 CISPEP 2 GLU A 148 PRO A 149 0 7.73 CISPEP 3 SER B 7 PRO B 8 0 -0.92 CISPEP 4 SER B 94 PRO B 95 0 -4.29 CISPEP 5 TYR B 140 PRO B 141 0 2.01 CISPEP 6 LYS C 48 PRO C 49 0 -0.83 CISPEP 7 LYS D 48 PRO D 49 0 -3.20 CISPEP 8 PHE H 146 PRO H 147 0 -6.49 CISPEP 9 GLU H 148 PRO H 149 0 7.37 CISPEP 10 SER L 7 PRO L 8 0 -8.02 CISPEP 11 SER L 94 PRO L 95 0 -2.29 CISPEP 12 TYR L 140 PRO L 141 0 -5.33 SITE 1 AC1 7 ARG C 82 HIS C 90 GLY C 92 GLU C 93 SITE 2 AC1 7 ARG L 18 HOH L 410 HOH L 413 CRYST1 87.406 313.892 51.127 90.00 90.00 90.00 P 21 21 2 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 0.011441 0.000000 0.000000 0.00000 SCALE2 0.000000 0.003186 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019559 0.00000