HEADER PROTEIN BINDING 16-APR-18 6D3O TITLE CRYSTAL STRUCTURE OF VASCULAR ENDOTHELIAL GROWTH FACTOR (VEGF8-109) TITLE 2 WITH HH4, AN ALPHA/BETA-PEPTIDE WITH IRREGULAR SECONDARY STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: VASCULAR ENDOTHELIAL GROWTH FACTOR A; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 34-135; COMPND 5 SYNONYM: VEGF-A,VASCULAR PERMEABILITY FACTOR,VPF; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: VASCULAR ENDOTHELIAL GROWTH FACTOR A; COMPND 9 CHAIN: B; COMPND 10 FRAGMENT: RESIDUES 34-135; COMPND 11 SYNONYM: VEGF-A,VASCULAR PERMEABILITY FACTOR,VPF; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: HH4 ALPHA/BETA-PEPTIDE; COMPND 15 CHAIN: C, D; COMPND 16 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: VEGFA, VEGF; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606; SOURCE 13 GENE: VEGFA, VEGF; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 15 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 16 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 17 MOL_ID: 3; SOURCE 18 SYNTHETIC: YES; SOURCE 19 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 20 ORGANISM_TAXID: 32630 KEYWDS ALPHA/BETA-PEPTIDE, VEGF, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR N.C.THOMAS,K.T.FOREST,S.H.GELLMAN REVDAT 8 15-NOV-23 6D3O 1 LINK ATOM REVDAT 7 25-OCT-23 6D3O 1 REMARK REVDAT 6 22-FEB-23 6D3O 1 COMPND SOURCE REMARK HELIX REVDAT 6 2 1 LINK ATOM REVDAT 5 24-FEB-21 6D3O 1 COMPND SOURCE REMARK DBREF REVDAT 5 2 1 SEQADV SEQRES HET HETNAM REVDAT 5 3 1 HETSYN FORMUL HELIX SHEET REVDAT 5 4 1 SSBOND LINK ATOM REVDAT 4 10-JUN-20 6D3O 1 AUTHOR JRNL REVDAT 3 01-JAN-20 6D3O 1 REMARK REVDAT 2 14-AUG-19 6D3O 1 JRNL SEQRES REVDAT 1 24-APR-19 6D3O 0 JRNL AUTH N.C.THOMAS,H.S.LONDON,K.T.FOREST,S.H.GELLMAN JRNL TITL HIGH-RESOLUTION STRUCTURES FOR A COMPLEX BETWEEN A JRNL TITL 2 NON-HELICAL FOLDAMER AND VEGF JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0267 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) : 3.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.29 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 6255 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) : 0.219 REMARK 3 R VALUE (WORKING SET) : 0.217 REMARK 3 FREE R VALUE : 0.279 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.300 REMARK 3 FREE R VALUE TEST SET COUNT : 279 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) : 3.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.18 REMARK 3 REFLECTION IN BIN (WORKING SET) : 462 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.3050 REMARK 3 BIN FREE R VALUE SET COUNT : 15 REMARK 3 BIN FREE R VALUE : 0.3030 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1720 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 2 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 66.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 77.41 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.06000 REMARK 3 B22 (A**2) : -1.06000 REMARK 3 B33 (A**2) : 3.44000 REMARK 3 B12 (A**2) : -0.53000 REMARK 3 B13 (A**2) : 0.00000 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): 0.460 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.360 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 39.682 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.922 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.877 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1772 ; 0.004 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 1591 ; 0.001 ; 0.018 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2404 ; 1.353 ; 1.703 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3688 ; 1.065 ; 1.629 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 204 ; 6.194 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 81 ;35.537 ;23.704 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 276 ;14.436 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 6 ;22.188 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 235 ; 0.046 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1954 ; 0.004 ; 0.019 REMARK 3 GENERAL PLANES OTHERS (A): 382 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 1 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 13 106 B 13 106 2321 0.120 0.050 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 14 A 107 REMARK 3 ORIGIN FOR THE GROUP (A): 32.3792 -35.9394 6.6183 REMARK 3 T TENSOR REMARK 3 T11: 0.0779 T22: 0.1146 REMARK 3 T33: 0.0334 T12: 0.0059 REMARK 3 T13: -0.0262 T23: 0.0450 REMARK 3 L TENSOR REMARK 3 L11: 2.7675 L22: 7.0701 REMARK 3 L33: 2.0858 L12: 2.0894 REMARK 3 L13: -0.0203 L23: 1.2976 REMARK 3 S TENSOR REMARK 3 S11: 0.4077 S12: 0.2728 S13: -0.0198 REMARK 3 S21: 0.6088 S22: -0.2577 S23: -0.3749 REMARK 3 S31: 0.0721 S32: -0.0608 S33: -0.1500 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 13 B 107 REMARK 3 ORIGIN FOR THE GROUP (A): 16.9601 -40.2532 3.1370 REMARK 3 T TENSOR REMARK 3 T11: 0.1038 T22: 0.4704 REMARK 3 T33: 0.1883 T12: -0.0219 REMARK 3 T13: 0.0850 T23: -0.1263 REMARK 3 L TENSOR REMARK 3 L11: 2.6559 L22: 7.0763 REMARK 3 L33: 1.8710 L12: -0.1686 REMARK 3 L13: 0.6699 L23: 1.8782 REMARK 3 S TENSOR REMARK 3 S11: 0.2380 S12: 0.1855 S13: -0.0420 REMARK 3 S21: 0.6784 S22: -0.6086 S23: 1.0864 REMARK 3 S31: 0.1845 S32: -0.6227 S33: 0.3706 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 U VALUES : WITH TLS ADDED REMARK 4 REMARK 4 6D3O COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-APR-18. REMARK 100 THE DEPOSITION ID IS D_1000233773. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-MAR-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL 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-F REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97872 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7198 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.000 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 (%) : 100.0 REMARK 200 DATA REDUNDANCY : 11.10 REMARK 200 R MERGE (I) : 0.14900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 11.30 REMARK 200 R MERGE FOR SHELL (I) : 1.43000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.700 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: 1VPF REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.76 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M AMMONIUM ACETATE, 0.1 M BIS-TRIS REMARK 280 PH 5.5, 17% W/V PEG 10000, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/2 REMARK 290 6555 X-Y,X,Z+1/2 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 0.00000 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 0.00000 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 29.99400 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 29.99400 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 29.99400 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 GLY A 8 REMARK 465 GLN A 9 REMARK 465 ASN A 10 REMARK 465 HIS A 11 REMARK 465 HIS A 12 REMARK 465 ASP A 109 REMARK 465 GLY B 8 REMARK 465 GLN B 9 REMARK 465 ASN B 10 REMARK 465 HIS B 11 REMARK 465 HIS B 12 REMARK 465 LYS B 108 REMARK 465 ASP B 109 REMARK 465 ASN D 4 REMARK 465 ARG D 18 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 GLU A 42 OE1 OE2 REMARK 470 GLU A 44 CG CD OE1 OE2 REMARK 470 ASP A 63 CG OD1 OD2 REMARK 470 GLU A 64 CG CD OE1 OE2 REMARK 470 GLU A 72 CG CD OE1 OE2 REMARK 470 GLU A 73 OE1 OE2 REMARK 470 ARG A 82 NE CZ NH1 NH2 REMARK 470 LYS A 84 CE NZ REMARK 470 LYS B 16 CG CD CE NZ REMARK 470 ASP B 19 CG OD1 OD2 REMARK 470 GLU B 30 CD OE1 OE2 REMARK 470 PHE B 36 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ASP B 41 CG OD1 OD2 REMARK 470 TYR B 45 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 GLU B 64 CG CD OE1 OE2 REMARK 470 GLU B 72 CG CD OE1 OE2 REMARK 470 LYS B 84 CG CD CE NZ REMARK 470 HIS B 86 CG ND1 CD2 CE1 NE2 REMARK 470 LYS B 101 CG CD CE NZ REMARK 470 GLU B 103 CG CD OE1 OE2 REMARK 470 ARG C 18 CG CD NE CZ NH1 NH2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 XPC C 17 C - N - CA ANGL. DEV. = 15.4 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 CYS A 26 108.00 -31.41 REMARK 500 CYS B 26 108.16 -30.53 REMARK 500 HT7 C 11 -24.47 90.52 REMARK 500 B3E C 14 8.35 -55.62 REMARK 500 HT7 D 11 -26.23 106.15 REMARK 500 B3E D 14 -4.71 -50.34 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 NLE C 10 HT7 C 11 135.36 REMARK 500 B3E C 14 CYS C 15 145.91 REMARK 500 PHE C 16 XPC C 17 140.85 REMARK 500 NLE D 10 HT7 D 11 135.80 REMARK 500 B3E D 14 CYS D 15 144.21 REMARK 500 PHE D 16 XPC D 17 140.73 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 B3E C 14 -15.52 REMARK 500 B3E D 14 -17.06 REMARK 500 REMARK 500 REMARK: NULL DBREF 6D3O A 8 109 UNP P15692 VEGFA_HUMAN 34 135 DBREF 6D3O B 8 109 UNP P15692 VEGFA_HUMAN 34 135 DBREF 6D3O C 4 18 PDB 6D3O 6D3O 4 18 DBREF 6D3O D 4 18 PDB 6D3O 6D3O 4 18 SEQADV 6D3O GLN A 23 UNP P15692 ARG 49 CONFLICT SEQADV 6D3O GLU A 89 UNP P15692 GLN 115 CONFLICT SEQADV 6D3O ALA A 108 UNP P15692 LYS 134 CONFLICT SEQRES 1 A 102 GLY GLN ASN HIS HIS GLU VAL VAL LYS PHE MET ASP VAL SEQRES 2 A 102 TYR GLN GLN SER TYR CYS HIS PRO ILE GLU THR LEU VAL SEQRES 3 A 102 ASP ILE PHE GLN GLU TYR PRO ASP GLU ILE GLU TYR ILE SEQRES 4 A 102 PHE LYS PRO SER CYS VAL PRO LEU MET ARG CYS GLY GLY SEQRES 5 A 102 CYS CYS ASN ASP GLU GLY LEU GLU CYS VAL PRO THR GLU SEQRES 6 A 102 GLU SER ASN ILE THR MET GLN ILE MET ARG ILE LYS PRO SEQRES 7 A 102 HIS GLN GLY GLU HIS ILE GLY GLU MET SER PHE LEU GLN SEQRES 8 A 102 HIS ASN LYS CYS GLU CYS ARG PRO LYS ALA ASP SEQRES 1 B 102 GLY GLN ASN HIS HIS GLU VAL VAL LYS PHE MET ASP VAL SEQRES 2 B 102 TYR GLN ARG SER TYR CYS HIS PRO ILE GLU THR LEU VAL SEQRES 3 B 102 ASP ILE PHE GLN GLU TYR PRO ASP GLU ILE GLU TYR ILE SEQRES 4 B 102 PHE LYS PRO SER CYS VAL PRO LEU MET ARG CYS GLY GLY SEQRES 5 B 102 CYS CYS ASN ASP GLU GLY LEU GLU CYS VAL PRO THR GLU SEQRES 6 B 102 GLU SER ASN ILE THR MET GLN ILE MET ARG ILE LYS PRO SEQRES 7 B 102 HIS GLN GLY GLN HIS ILE GLY GLU MET SER PHE LEU GLN SEQRES 8 B 102 HIS ASN LYS CYS GLU CYS ARG PRO LYS LYS ASP SEQRES 1 C 15 ASN CYS ASP ILE HIS VAL NLE HT7 GLU TRP B3E CYS PHE SEQRES 2 C 15 XPC ARG SEQRES 1 D 15 ASN CYS ASP ILE HIS VAL NLE HT7 GLU TRP B3E CYS PHE SEQRES 2 D 15 XPC ARG HET NLE C 10 8 HET HT7 C 11 15 HET B3E C 14 10 HET XPC C 17 8 HET NLE D 10 8 HET HT7 D 11 15 HET B3E D 14 10 HET XPC D 17 8 HETNAM NLE NORLEUCINE HETNAM HT7 (3S)-3-AMINO-4-(1H-INDOL-3-YL)BUTANOIC ACID HETNAM B3E (3S)-3-AMINOHEXANEDIOIC ACID HETNAM XPC (3S,4R)-4-AMINOPYRROLIDINE-3-CARBOXYLIC ACID HETSYN HT7 BETA-HOMOTRYPTOPHAN HETSYN XPC (3R,4S)-3-AMINOPYRROLIDINE-4-CARBOXYLIC ACID FORMUL 3 NLE 2(C6 H13 N O2) FORMUL 3 HT7 2(C12 H14 N2 O2) FORMUL 3 B3E 2(C6 H11 N O4) FORMUL 3 XPC 2(C5 H10 N2 O2) FORMUL 5 HOH *2(H2 O) HELIX 1 AA1 LYS A 16 TYR A 25 1 10 HELIX 2 AA2 PHE A 36 GLU A 38 5 3 HELIX 3 AA3 LYS B 16 TYR B 25 1 10 HELIX 4 AA4 PHE B 36 GLU B 38 5 3 HELIX 5 AA5 GLU C 12 XPC C 17 1 6 HELIX 6 AA6 GLU D 12 XPC D 17 1 6 SHEET 1 AA1 2 HIS A 27 ASP A 34 0 SHEET 2 AA1 2 CYS A 51 GLY A 58 -1 O LEU A 54 N THR A 31 SHEET 1 AA2 3 ILE A 46 LYS A 48 0 SHEET 2 AA2 3 LEU A 66 LYS A 84 -1 O ILE A 83 N ILE A 46 SHEET 3 AA2 3 GLY A 88 PRO A 106 -1 O HIS A 90 N ARG A 82 SHEET 1 AA3 2 HIS B 27 ASP B 34 0 SHEET 2 AA3 2 CYS B 51 GLY B 58 -1 O LEU B 54 N THR B 31 SHEET 1 AA4 3 ILE B 46 LYS B 48 0 SHEET 2 AA4 3 LEU B 66 LYS B 84 -1 O ILE B 83 N ILE B 46 SHEET 3 AA4 3 GLY B 88 PRO B 106 -1 O HIS B 90 N ARG B 82 SSBOND 1 CYS A 26 CYS A 68 1555 1555 2.03 SSBOND 2 CYS A 57 CYS A 102 1555 1555 2.03 SSBOND 3 CYS A 61 CYS A 104 1555 1555 2.05 SSBOND 4 CYS B 26 CYS B 68 1555 1555 2.04 SSBOND 5 CYS B 57 CYS B 102 1555 1555 2.04 SSBOND 6 CYS B 61 CYS B 104 1555 1555 2.05 SSBOND 7 CYS C 5 CYS C 15 1555 1555 2.04 LINK C VAL C 9 N NLE C 10 1555 1555 1.34 LINK C NLE C 10 N HT7 C 11 1555 1555 1.34 LINK C HT7 C 11 N GLU C 12 1555 1555 1.36 LINK C TRP C 13 N B3E C 14 1555 1555 1.32 LINK C B3E C 14 N CYS C 15 1555 1555 1.37 LINK C PHE C 16 N XPC C 17 1555 1555 1.33 LINK C XPC C 17 N ARG C 18 1555 1555 1.37 LINK C VAL D 9 N NLE D 10 1555 1555 1.34 LINK C NLE D 10 N HT7 D 11 1555 1555 1.33 LINK C HT7 D 11 N GLU D 12 1555 1555 1.37 LINK C TRP D 13 N B3E D 14 1555 1555 1.33 LINK C B3E D 14 N CYS D 15 1555 1555 1.37 LINK C PHE D 16 N XPC D 17 1555 1555 1.34 CISPEP 1 LYS A 48 PRO A 49 0 -8.04 CISPEP 2 LYS B 48 PRO B 49 0 -7.15 CRYST1 101.649 101.649 59.988 90.00 90.00 120.00 P 63 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 0.009838 0.005680 0.000000 0.00000 SCALE2 0.000000 0.011360 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016670 0.00000 MTRIX1 1 1.000000 0.000000 0.000000 0.00000 1 MTRIX2 1 0.000000 1.000000 0.000000 0.00000 1 MTRIX3 1 0.000000 0.000000 1.000000 0.00000 1 MTRIX1 2 -0.901000 0.074558 -0.427365 51.24354 1 MTRIX2 2 0.070948 -0.946533 -0.314710 -74.59712 1 MTRIX3 2 -0.427979 -0.313875 0.847536 -1.40020 1 MTRIX1 3 1.000000 0.000000 0.000000 0.00000 1 MTRIX2 3 0.000000 1.000000 0.000000 0.00000 1 MTRIX3 3 0.000000 0.000000 1.000000 0.00000 1 MTRIX1 4 -0.943656 0.047152 -0.327552 51.10066 1 MTRIX2 4 0.046021 -0.961481 -0.270991 -74.64796 1 MTRIX3 4 -0.327713 -0.270796 0.905137 -1.69968 1