HEADER IMMUNE SYSTEM 13-OCT-20 7KEZ TITLE CRYSTAL STRUCTURE OF BH1 FAB VARIANT (CDR H3 LOOP DESIGN 16_0325) IN TITLE 2 COMPLEX WITH VEGF COMPND MOL_ID: 1; COMPND 2 MOLECULE: ANTI-VEGF-A FAB BH1 HEAVY CHAIN; COMPND 3 CHAIN: H; COMPND 4 FRAGMENT: FAB FRAGMENT HEAVY CHAIN; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: ANTI-VEGF-A FAB BH1 LIGHT CHAIN; COMPND 9 CHAIN: L; COMPND 10 FRAGMENT: FAB FRAGMENT LIGHT CHAIN; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: ISOFORM L-VEGF206 OF VASCULAR ENDOTHELIAL GROWTH FACTOR A; COMPND 14 CHAIN: V; COMPND 15 FRAGMENT: VASCULAR ENDOTHELIAL GROWTH FACTOR A; COMPND 16 SYNONYM: VEGF-A,VASCULAR PERMEABILITY FACTOR,VPF; COMPND 17 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_TAXID: 9606; SOURCE 4 EXPRESSION_SYSTEM: CRICETULUS GRISEUS; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 10029; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: CHO-3E7; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 9 ORGANISM_TAXID: 9606; SOURCE 10 EXPRESSION_SYSTEM: CRICETULUS GRISEUS; SOURCE 11 EXPRESSION_SYSTEM_TAXID: 10029; SOURCE 12 MOL_ID: 3; SOURCE 13 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 14 ORGANISM_COMMON: HUMAN; SOURCE 15 ORGANISM_TAXID: 9606; SOURCE 16 GENE: VEGFA, VEGF; SOURCE 17 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 18 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 19 EXPRESSION_SYSTEM_CELL_LINE: HEK293-6E; SOURCE 20 EXPRESSION_SYSTEM_VECTOR_TYPE: PTT5 KEYWDS FAB-ANTIGEN COMPLEX, CDR H3 LOOP, VEGF, ANTIBODY DESIGN, IMMUNE KEYWDS 2 SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR R.SHI,M.S.MANENDA,M.-E.PICARD REVDAT 2 18-OCT-23 7KEZ 1 REMARK REVDAT 1 10-NOV-21 7KEZ 0 JRNL AUTH M.-E.PICARD,M.S.MANENDA,C.CORBEIL,T.SULEA,J.BAARDSNESS, JRNL AUTH 2 H.HOGUES,F.GAUDREAULT,C.DEPREZ,E.O.PURISIMA,R.SHI JRNL TITL CRYSTAL STRUCTURE OF BH1 FAB CDR H3 LOOP VARIANTS IN APO JRNL TITL 2 FORM AND IN COMPLEX WITH VEGF JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH C.CORBEIL,M.S.MANENDA,T.SULEA,J.BAARDSNESS,M.-E.PICARD, REMARK 1 AUTH 2 H.HOGUES,F.GAUDREAULT,C.DEPREZ,R.SHI,E.O.PURISIMA REMARK 1 TITL ADAPTING ANTIBODY H3 LOOPS TO COGNATE ANTIGENS USING HUMAN REMARK 1 TITL 2 GERMLINE DERIVED SEQUENCES REMARK 1 REF TO BE PUBLISHED REMARK 1 REFN REMARK 2 REMARK 2 RESOLUTION. 2.31 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0135 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.31 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 96.92 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 31562 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) : 0.181 REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1654 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.31 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.37 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2284 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.75 REMARK 3 BIN R VALUE (WORKING SET) : 0.2780 REMARK 3 BIN FREE R VALUE SET COUNT : 126 REMARK 3 BIN FREE R VALUE : 0.3420 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4073 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 246 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 56.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.11000 REMARK 3 B22 (A**2) : -1.93000 REMARK 3 B33 (A**2) : 2.04000 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): 0.230 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.205 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.154 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.506 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.961 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.941 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4188 ; 0.017 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3841 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5693 ; 1.793 ; 1.948 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8890 ; 1.046 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 528 ; 7.716 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 173 ;36.016 ;24.104 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 670 ;17.560 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 19 ;21.225 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 629 ; 0.107 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4728 ; 0.009 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 947 ; 0.002 ; 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 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 U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 7KEZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-OCT-20. REMARK 100 THE DEPOSITION ID IS D_1000252374. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-JUN-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CLSI REMARK 200 BEAMLINE : 08ID-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-300 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA 0.6.3 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33259 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.310 REMARK 200 RESOLUTION RANGE LOW (A) : 96.920 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : 0.08700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.31 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.39 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 7.00 REMARK 200 R MERGE FOR SHELL (I) : 0.94600 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: MOLREP REMARK 200 STARTING MODEL: 3BDY 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 HEPES PH 7.5, 20 %(W/V) PEG REMARK 280 4000, 10 %(W/V) ISOPROPANOL, MICROBATCH, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 38.18950 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 38.18950 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 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 50.39950 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 96.91950 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 50.39950 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 96.91950 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 38.18950 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 50.39950 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 96.91950 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 38.18950 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 50.39950 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 96.91950 REMARK 290 SMTRY3 8 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 APPLY THE FOLLOWING TO CHAINS: H, L, V 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 APPLY THE FOLLOWING TO CHAINS: H, L, V REMARK 350 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 -193.83900 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH L 352 LIES ON A SPECIAL POSITION. 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 H 127 REMARK 465 SER H 128 REMARK 465 LYS H 129 REMARK 465 SER H 130 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 GLY H 220 REMARK 465 HIS H 221 REMARK 465 HIS H 222 REMARK 465 HIS H 223 REMARK 465 HIS H 224 REMARK 465 HIS H 225 REMARK 465 HIS H 226 REMARK 465 HIS H 227 REMARK 465 HIS H 228 REMARK 465 GLY H 229 REMARK 465 GLU L 213 REMARK 465 CYS L 214 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 LYS V 107 REMARK 465 LYS V 108 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 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 SER L 9 CB SER L 9 OG -0.107 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 H 50 NE - CZ - NH1 ANGL. DEV. = -5.0 DEGREES REMARK 500 ARG H 50 NE - CZ - NH2 ANGL. DEV. = 3.1 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 ALA H 88 163.17 176.35 REMARK 500 ASP H 144 80.03 60.80 REMARK 500 SER L 52 17.41 -153.17 REMARK 500 ALA L 84 168.50 178.38 REMARK 500 LYS L 126 -119.03 -51.01 REMARK 500 SER L 127 -60.33 31.85 REMARK 500 ASN L 152 -18.68 69.18 REMARK 500 ALA L 184 -73.66 -39.04 REMARK 500 LYS L 190 -60.11 -106.14 REMARK 500 ARG L 211 107.25 -49.59 REMARK 500 CYS V 26 111.39 -7.29 REMARK 500 ASN V 62 48.43 72.31 REMARK 500 ASP V 63 90.00 -172.46 REMARK 500 GLU V 64 -36.01 -35.31 REMARK 500 THR V 71 -60.88 -100.53 REMARK 500 HIS V 86 12.49 59.87 REMARK 500 GLN V 87 -55.19 -128.34 REMARK 500 REMARK 500 REMARK: NULL DBREF 7KEZ H 1 229 PDB 7KEZ 7KEZ 1 229 DBREF 7KEZ L 1 214 PDB 7KEZ 7KEZ 1 214 DBREF1 7KEZ V 1 110 UNP VEGFA-14_HUMAN DBREF2 7KEZ V P15692-14 207 316 SEQADV 7KEZ HIS V 111 UNP P15692-14 EXPRESSION TAG SEQADV 7KEZ HIS V 112 UNP P15692-14 EXPRESSION TAG SEQADV 7KEZ HIS V 113 UNP P15692-14 EXPRESSION TAG SEQADV 7KEZ HIS V 114 UNP P15692-14 EXPRESSION TAG SEQADV 7KEZ HIS V 115 UNP P15692-14 EXPRESSION TAG SEQADV 7KEZ HIS V 116 UNP P15692-14 EXPRESSION TAG SEQRES 1 H 239 GLU VAL GLN LEU VAL GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 H 239 PRO GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 H 239 PHE ASN ILE LYS ASP THR TYR ILE HIS TRP VAL ARG GLN SEQRES 4 H 239 ALA PRO GLY LYS GLY LEU GLU TRP VAL ALA ARG ILE TYR SEQRES 5 H 239 PRO THR ASN GLY TYR THR ARG TYR ALA ASP SER VAL LYS SEQRES 6 H 239 GLY ARG PHE THR ILE SER ALA ASP THR SER LYS ASN THR SEQRES 7 H 239 ALA TYR LEU GLN MET ASN SER LEU ARG ALA GLU ASP THR SEQRES 8 H 239 ALA VAL TYR TYR CYS ALA ARG GLY GLY ALA VAL ALA GLY SEQRES 9 H 239 THR GLY VAL TYR TYR PHE ASP TYR TRP GLY GLN GLY THR SEQRES 10 H 239 LEU VAL THR VAL SER SER ALA SER THR LYS GLY PRO SER SEQRES 11 H 239 VAL PHE PRO LEU ALA PRO SER SER LYS SER THR SER GLY SEQRES 12 H 239 GLY THR ALA ALA LEU GLY CYS LEU VAL LYS ASP TYR PHE SEQRES 13 H 239 PRO GLU PRO VAL THR VAL SER TRP ASN SER GLY ALA LEU SEQRES 14 H 239 THR SER GLY VAL HIS THR PHE PRO ALA VAL LEU GLN SER SEQRES 15 H 239 SER GLY LEU TYR SER LEU SER SER VAL VAL THR VAL PRO SEQRES 16 H 239 SER SER SER LEU GLY THR GLN THR TYR ILE CYS ASN VAL SEQRES 17 H 239 ASN HIS LYS PRO SER ASN THR LYS VAL ASP LYS LYS VAL SEQRES 18 H 239 GLU PRO LYS SER CYS ASP LYS THR GLY HIS HIS HIS HIS SEQRES 19 H 239 HIS HIS HIS HIS GLY SEQRES 1 L 218 ASP ILE GLN MET THR GLN SER PRO SER SER LEU SER ALA SEQRES 2 L 218 SER VAL GLY ASP ARG VAL THR ILE THR CYS ARG ALA SER SEQRES 3 L 218 GLN ASP ILE PRO ARG SER ILE SER GLY TYR VAL ALA TRP SEQRES 4 L 218 TYR GLN GLN LYS PRO GLY LYS ALA PRO LYS LEU LEU ILE SEQRES 5 L 218 TYR TRP GLY SER TYR LEU TYR SER GLY VAL PRO SER ARG SEQRES 6 L 218 PHE SER GLY SER GLY SER GLY THR ASP PHE THR LEU THR SEQRES 7 L 218 ILE SER SER LEU GLN PRO GLU ASP PHE ALA THR TYR TYR SEQRES 8 L 218 CYS GLN GLN HIS TYR THR THR PRO PRO THR PHE GLY GLN SEQRES 9 L 218 GLY THR LYS VAL GLU ILE LYS ARG THR VAL ALA ALA PRO SEQRES 10 L 218 SER VAL PHE ILE PHE PRO PRO SER ASP GLU GLN LEU LYS SEQRES 11 L 218 SER GLY THR ALA SER VAL VAL CYS LEU LEU ASN ASN PHE SEQRES 12 L 218 TYR PRO ARG GLU ALA LYS VAL GLN TRP LYS VAL ASP ASN SEQRES 13 L 218 ALA LEU GLN SER GLY ASN SER GLN GLU SER VAL THR GLU SEQRES 14 L 218 GLN ASP SER LYS ASP SER THR TYR SER LEU SER SER THR SEQRES 15 L 218 LEU THR LEU SER LYS ALA ASP TYR GLU LYS HIS LYS VAL SEQRES 16 L 218 TYR ALA CYS GLU VAL THR HIS GLN GLY LEU SER SER PRO SEQRES 17 L 218 VAL THR LYS SER PHE ASN ARG GLY GLU CYS 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 HET CL H 300 1 HETNAM CL CHLORIDE ION FORMUL 4 CL CL 1- FORMUL 5 HOH *246(H2 O) HELIX 1 AA1 ASN H 28 THR H 32 5 5 HELIX 2 AA2 THR H 73 LYS H 75 5 3 HELIX 3 AA3 ARG H 83 THR H 87 5 5 HELIX 4 AA4 SER H 187 THR H 191 5 5 HELIX 5 AA5 LYS H 201 ASN H 204 5 4 HELIX 6 AA6 GLN L 79 PHE L 83 5 5 HELIX 7 AA7 SER L 121 LYS L 126 1 6 HELIX 8 AA8 LYS L 183 LYS L 188 1 6 HELIX 9 AA9 LYS V 16 TYR V 25 1 10 HELIX 10 AB1 ILE V 35 TYR V 39 1 5 SHEET 1 AA1 4 GLN H 3 SER H 7 0 SHEET 2 AA1 4 LEU H 18 SER H 25 -1 O SER H 21 N SER H 7 SHEET 3 AA1 4 THR H 77 MET H 82 -1 O MET H 82 N LEU H 18 SHEET 4 AA1 4 PHE H 67 ASP H 72 -1 N THR H 68 O GLN H 81 SHEET 1 AA2 6 GLY H 10 VAL H 12 0 SHEET 2 AA2 6 THR H 107 VAL H 111 1 O THR H 110 N VAL H 12 SHEET 3 AA2 6 ALA H 88 GLY H 95 -1 N TYR H 90 O THR H 107 SHEET 4 AA2 6 TYR H 33 GLN H 39 -1 N VAL H 37 O TYR H 91 SHEET 5 AA2 6 GLU H 46 TYR H 52 -1 O GLU H 46 N ARG H 38 SHEET 6 AA2 6 TYR H 56 TYR H 59 -1 O ARG H 58 N ARG H 50 SHEET 1 AA3 4 GLY H 10 VAL H 12 0 SHEET 2 AA3 4 THR H 107 VAL H 111 1 O THR H 110 N VAL H 12 SHEET 3 AA3 4 ALA H 88 GLY H 95 -1 N TYR H 90 O THR H 107 SHEET 4 AA3 4 TYR H 102 TRP H 103 -1 O TYR H 102 N ARG H 94 SHEET 1 AA4 2 ALA H 97 VAL H 98 0 SHEET 2 AA4 2 THR H 100A GLY H 100B-1 O THR H 100A N VAL H 98 SHEET 1 AA5 4 SER H 120 LEU H 124 0 SHEET 2 AA5 4 THR H 135 TYR H 145 -1 O LEU H 141 N PHE H 122 SHEET 3 AA5 4 TYR H 176 PRO H 185 -1 O LEU H 178 N VAL H 142 SHEET 4 AA5 4 VAL H 163 THR H 165 -1 N HIS H 164 O VAL H 181 SHEET 1 AA6 4 SER H 120 LEU H 124 0 SHEET 2 AA6 4 THR H 135 TYR H 145 -1 O LEU H 141 N PHE H 122 SHEET 3 AA6 4 TYR H 176 PRO H 185 -1 O LEU H 178 N VAL H 142 SHEET 4 AA6 4 VAL H 169 LEU H 170 -1 N VAL H 169 O SER H 177 SHEET 1 AA7 3 THR H 151 TRP H 154 0 SHEET 2 AA7 3 ILE H 195 HIS H 200 -1 O ASN H 199 N THR H 151 SHEET 3 AA7 3 THR H 205 LYS H 210 -1 O VAL H 207 N VAL H 198 SHEET 1 AA8 4 MET L 4 SER L 7 0 SHEET 2 AA8 4 VAL L 19 ALA L 25 -1 O THR L 22 N SER L 7 SHEET 3 AA8 4 ASP L 70 ILE L 75 -1 O ILE L 75 N VAL L 19 SHEET 4 AA8 4 PHE L 62 SER L 67 -1 N SER L 65 O THR L 72 SHEET 1 AA9 6 SER L 10 SER L 14 0 SHEET 2 AA9 6 THR L 102 LYS L 107 1 O LYS L 107 N ALA L 13 SHEET 3 AA9 6 ALA L 84 GLN L 90 -1 N ALA L 84 O VAL L 104 SHEET 4 AA9 6 VAL L 33 GLN L 38 -1 N GLN L 38 O THR L 85 SHEET 5 AA9 6 LYS L 45 TYR L 49 -1 O LEU L 47 N TRP L 35 SHEET 6 AA9 6 TYR L 53 LEU L 54 -1 O TYR L 53 N TYR L 49 SHEET 1 AB1 4 SER L 10 SER L 14 0 SHEET 2 AB1 4 THR L 102 LYS L 107 1 O LYS L 107 N ALA L 13 SHEET 3 AB1 4 ALA L 84 GLN L 90 -1 N ALA L 84 O VAL L 104 SHEET 4 AB1 4 THR L 97 PHE L 98 -1 O THR L 97 N GLN L 90 SHEET 1 AB2 4 ILE L 29 SER L 30 0 SHEET 2 AB2 4 GLY V 88 ARG V 105 -1 O ILE V 91 N SER L 30 SHEET 3 AB2 4 GLU V 67 LYS V 84 -1 N MET V 78 O MET V 94 SHEET 4 AB2 4 ILE V 46 LYS V 48 -1 N LYS V 48 O MET V 81 SHEET 1 AB3 4 SER L 114 PHE L 118 0 SHEET 2 AB3 4 THR L 129 PHE L 139 -1 O ASN L 137 N SER L 114 SHEET 3 AB3 4 TYR L 173 SER L 182 -1 O LEU L 179 N VAL L 132 SHEET 4 AB3 4 SER L 159 VAL L 163 -1 N SER L 162 O SER L 176 SHEET 1 AB4 4 ALA L 153 LEU L 154 0 SHEET 2 AB4 4 LYS L 145 VAL L 150 -1 N VAL L 150 O ALA L 153 SHEET 3 AB4 4 VAL L 191 THR L 197 -1 O GLU L 195 N GLN L 147 SHEET 4 AB4 4 VAL L 205 ASN L 210 -1 O VAL L 205 N VAL L 196 SHEET 1 AB5 2 HIS V 27 ASP V 34 0 SHEET 2 AB5 2 CYS V 51 GLY V 58 -1 O LEU V 54 N THR V 31 SSBOND 1 CYS H 22 CYS H 92 1555 1555 2.16 SSBOND 2 CYS H 140 CYS H 196 1555 1555 2.03 SSBOND 3 CYS L 23 CYS L 88 1555 1555 2.09 SSBOND 4 CYS L 134 CYS L 194 1555 1555 2.00 SSBOND 5 CYS V 26 CYS V 68 1555 1555 2.07 SSBOND 6 CYS V 51 CYS V 60 1555 4545 2.90 SSBOND 7 CYS V 57 CYS V 102 1555 1555 2.05 SSBOND 8 CYS V 61 CYS V 104 1555 1555 2.09 CISPEP 1 PHE H 146 PRO H 147 0 -11.25 CISPEP 2 GLU H 148 PRO H 149 0 -0.24 CISPEP 3 SER L 7 PRO L 8 0 -12.30 CISPEP 4 THR L 94 PRO L 95 0 -2.08 CISPEP 5 TYR L 140 PRO L 141 0 -4.14 CISPEP 6 LYS V 48 PRO V 49 0 -14.83 CRYST1 100.799 193.839 76.379 90.00 90.00 90.00 C 2 2 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 0.009921 0.000000 0.000000 0.00000 SCALE2 0.000000 0.005159 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013093 0.00000