HEADER PROTEIN BINDING 08-DEC-19 6V7K TITLE CRYSTAL STRUCTURE OF VASCULAR ENDOTHELIAL GROWTH FACTOR (VEGF8-109) TITLE 2 WITH ONE COPY OF HH4, AN ALPHA/BETA-PEPTIDE WITH IRREGULAR SECONDARY TITLE 3 STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: VASCULAR ENDOTHELIAL GROWTH FACTOR A; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: VEGF-A,VASCULAR PERMEABILITY FACTOR,VPF; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: ALPHA/BETA-PEPTIDE HH4; COMPND 8 CHAIN: X; COMPND 9 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 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 12 ORGANISM_TAXID: 32630 KEYWDS PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR N.C.THOMAS,K.T.FOREST,S.H.GELLMAN REVDAT 5 15-NOV-23 6V7K 1 LINK ATOM REVDAT 4 25-OCT-23 6V7K 1 REMARK REVDAT 3 22-FEB-23 6V7K 1 COMPND SOURCE REMARK SEQRES REVDAT 3 2 1 HET HETNAM HETSYN FORMUL REVDAT 2 16-MAR-22 6V7K 1 REMARK REVDAT 1 09-DEC-20 6V7K 0 JRNL AUTH N.C.THOMAS,K.T.FOREST,S.H.GELLMAN JRNL TITL HIGH-RESOLUTION STRUCTURE FOR A COMPLEX BETWEEN ONE COPY OF JRNL TITL 2 A NON-HELICAL FOLDAMER AND VEGF JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0222 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.50 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 12935 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.246 REMARK 3 R VALUE (WORKING SET) : 0.244 REMARK 3 FREE R VALUE : 0.278 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 681 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.57 REMARK 3 REFLECTION IN BIN (WORKING SET) : 928 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.09 REMARK 3 BIN R VALUE (WORKING SET) : 0.3800 REMARK 3 BIN FREE R VALUE SET COUNT : NULL REMARK 3 BIN FREE R VALUE : 0.4360 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1562 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) : 65.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 48.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 7.75000 REMARK 3 B22 (A**2) : -4.42000 REMARK 3 B33 (A**2) : -3.33000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.303 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.247 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.236 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : NULL REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): NULL ; NULL ; NULL REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): NULL ; NULL ; NULL REMARK 3 GENERAL PLANES REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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 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 : NULL 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: NULL REMARK 4 REMARK 4 6V7K COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-DEC-19. REMARK 100 THE DEPOSITION ID IS D_1000244352. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-JUN-14 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-G 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 : 13653 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 37.510 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : 0.09700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.64 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.4 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.58300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.200 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 (%): 68.13 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.86 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 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 28.69000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 42.86000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 38.77850 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 42.86000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.69000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 38.77850 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, 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 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 7 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 LYS A 108 REMARK 465 ASP A 109 REMARK 465 MET B 7 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 1VR X 1 REMARK 465 GLU X 2 REMARK 465 XCP X 3 REMARK 465 ASN X 4 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 13 CG CD OE1 OE2 REMARK 470 LYS A 16 CG CD CE NZ REMARK 470 ASP A 41 CG OD1 OD2 REMARK 470 GLU A 42 CD OE1 OE2 REMARK 470 ILE A 43 CG1 CG2 CD1 REMARK 470 GLU A 44 CG CD OE1 OE2 REMARK 470 TYR A 45 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 GLU A 64 CG CD OE1 OE2 REMARK 470 ARG A 82 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 84 CG CD CE NZ REMARK 470 HIS A 86 CG ND1 CD2 CE1 NE2 REMARK 470 GLN A 87 CG CD OE1 NE2 REMARK 470 GLN A 89 CG CD OE1 NE2 REMARK 470 LYS A 101 CG CD CE NZ REMARK 470 LYS A 107 CG CD CE NZ REMARK 470 GLU B 13 CG CD OE1 OE2 REMARK 470 LYS B 16 CE NZ REMARK 470 ASP B 41 CG OD1 OD2 REMARK 470 GLU B 44 CG CD OE1 OE2 REMARK 470 GLU B 64 CG CD OE1 OE2 REMARK 470 GLU B 67 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 B 105 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 107 CG CD CE NZ REMARK 470 GLU X 12 CG CD OE1 OE2 REMARK 470 B3E X 14 CE OF2 OF1 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 OH TYR A 21 ND2 ASN A 62 2.02 REMARK 500 REMARK 500 REMARK: NULL 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 ARG X 18 C - N - CA ANGL. DEV. = 18.2 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 26 111.96 -15.72 REMARK 500 GLU A 42 45.88 -99.42 REMARK 500 CYS B 26 105.47 -8.97 REMARK 500 GLU B 42 38.60 -99.78 REMARK 500 HT7 X 11 -22.36 95.27 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 X 10 HT7 X 11 136.98 REMARK 500 B3E X 14 CYS X 15 144.57 REMARK 500 PHE X 16 XPC X 17 139.27 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 105 0.18 SIDE CHAIN REMARK 500 ARG B 56 0.09 SIDE CHAIN REMARK 500 ARG B 82 0.09 SIDE CHAIN REMARK 500 ARG X 18 0.09 SIDE CHAIN 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 X 14 -17.22 REMARK 500 REMARK 500 REMARK: NULL DBREF 6V7K A 8 109 UNP P15692 VEGFA_HUMAN 34 135 DBREF 6V7K B 8 109 UNP P15692 VEGFA_HUMAN 34 135 DBREF 6V7K X 1 19 PDB 6V7K 6V7K 1 19 SEQADV 6V7K MET A 7 UNP P15692 INITIATING METHIONINE SEQADV 6V7K MET B 7 UNP P15692 INITIATING METHIONINE SEQRES 1 A 103 MET GLY GLN ASN HIS HIS GLU VAL VAL LYS PHE MET ASP SEQRES 2 A 103 VAL TYR GLN ARG SER TYR CYS HIS PRO ILE GLU THR LEU SEQRES 3 A 103 VAL ASP ILE PHE GLN GLU TYR PRO ASP GLU ILE GLU TYR SEQRES 4 A 103 ILE PHE LYS PRO SER CYS VAL PRO LEU MET ARG CYS GLY SEQRES 5 A 103 GLY CYS CYS ASN ASP GLU GLY LEU GLU CYS VAL PRO THR SEQRES 6 A 103 GLU GLU SER ASN ILE THR MET GLN ILE MET ARG ILE LYS SEQRES 7 A 103 PRO HIS GLN GLY GLN HIS ILE GLY GLU MET SER PHE LEU SEQRES 8 A 103 GLN HIS ASN LYS CYS GLU CYS ARG PRO LYS LYS ASP SEQRES 1 B 103 MET GLY GLN ASN HIS HIS GLU VAL VAL LYS PHE MET ASP SEQRES 2 B 103 VAL TYR GLN ARG SER TYR CYS HIS PRO ILE GLU THR LEU SEQRES 3 B 103 VAL ASP ILE PHE GLN GLU TYR PRO ASP GLU ILE GLU TYR SEQRES 4 B 103 ILE PHE LYS PRO SER CYS VAL PRO LEU MET ARG CYS GLY SEQRES 5 B 103 GLY CYS CYS ASN ASP GLU GLY LEU GLU CYS VAL PRO THR SEQRES 6 B 103 GLU GLU SER ASN ILE THR MET GLN ILE MET ARG ILE LYS SEQRES 7 B 103 PRO HIS GLN GLY GLN HIS ILE GLY GLU MET SER PHE LEU SEQRES 8 B 103 GLN HIS ASN LYS CYS GLU CYS ARG PRO LYS LYS ASP SEQRES 1 X 19 1VR GLU XCP ASN CYS ASP ILE HIS VAL NLE HT7 GLU TRP SEQRES 2 X 19 B3E CYS PHE XPC ARG B3L HET NLE X 10 8 HET HT7 X 11 15 HET B3E X 14 7 HET XPC X 17 8 HET B3L X 19 9 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 HETNAM B3L (3S)-3-AMINO-5-METHYLHEXANOIC ACID HETSYN HT7 BETA-HOMOTRYPTOPHAN HETSYN XPC (3R,4S)-3-AMINOPYRROLIDINE-4-CARBOXYLIC ACID HETSYN B3L (S)-BETA-3-HOMOLEUCINE FORMUL 3 NLE C6 H13 N O2 FORMUL 3 HT7 C12 H14 N2 O2 FORMUL 3 B3E C6 H11 N O4 FORMUL 3 XPC C5 H10 N2 O2 FORMUL 3 B3L C7 H15 N O2 FORMUL 4 HOH *2(H2 O) HELIX 1 AA1 LYS A 16 TYR A 25 1 10 HELIX 2 AA2 ILE A 35 TYR A 39 1 5 HELIX 3 AA3 PRO A 40 ILE A 43 5 4 HELIX 4 AA4 LYS B 16 TYR B 25 1 10 HELIX 5 AA5 ILE B 35 TYR B 39 1 5 HELIX 6 AA6 PRO B 40 ILE B 43 5 4 HELIX 7 AA7 GLU X 12 ARG X 18 1 7 SHEET 1 AA1 2 HIS A 27 ASP A 34 0 SHEET 2 AA1 2 CYS A 51 GLY A 58 -1 O ARG A 56 N ILE A 29 SHEET 1 AA2 3 ILE A 46 LYS A 48 0 SHEET 2 AA2 3 LEU A 66 ILE A 83 -1 O ILE A 83 N ILE A 46 SHEET 3 AA2 3 GLN A 89 PRO A 106 -1 O ASN A 100 N GLU A 72 SHEET 1 AA3 2 HIS B 27 ASP B 34 0 SHEET 2 AA3 2 CYS B 51 GLY B 58 -1 O ARG B 56 N ILE B 29 SHEET 1 AA4 3 ILE B 46 LYS B 48 0 SHEET 2 AA4 3 LEU B 66 ILE B 83 -1 O MET B 81 N LYS B 48 SHEET 3 AA4 3 GLN B 89 PRO B 106 -1 O GLN B 98 N SER B 74 SSBOND 1 CYS A 26 CYS A 68 1555 1555 2.11 SSBOND 2 CYS A 57 CYS A 102 1555 1555 2.10 SSBOND 3 CYS A 60 CYS B 51 1555 1555 2.08 SSBOND 4 CYS A 61 CYS A 104 1555 1555 2.11 SSBOND 5 CYS B 26 CYS B 68 1555 1555 2.09 SSBOND 6 CYS B 57 CYS B 102 1555 1555 2.06 SSBOND 7 CYS B 61 CYS B 104 1555 1555 2.10 SSBOND 8 CYS X 5 CYS X 15 1555 1555 2.06 LINK C VAL X 9 N NLE X 10 1555 1555 1.33 LINK C NLE X 10 N HT7 X 11 1555 1555 1.34 LINK C HT7 X 11 N GLU X 12 1555 1555 1.35 LINK C TRP X 13 N B3E X 14 1555 1555 1.32 LINK C B3E X 14 N CYS X 15 1555 1555 1.36 LINK C PHE X 16 N XPC X 17 1555 1555 1.33 LINK C XPC X 17 N ARG X 18 1555 1555 1.31 LINK C ARG X 18 N B3L X 19 1555 1555 1.37 CISPEP 1 LYS A 48 PRO A 49 0 -10.95 CISPEP 2 LYS B 48 PRO B 49 0 -20.97 CRYST1 57.380 77.557 85.720 90.00 90.00 90.00 P 21 21 21 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 0.017428 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012894 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011666 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 0.914998 0.260050 0.308469 7.57759 1 MTRIX2 2 0.278152 -0.960413 -0.015408 -40.64958 1 MTRIX3 2 0.292251 0.099900 -0.951110 -13.00551 1