HEADER HORMONE/DNA 26-OCT-12 4HQU TITLE CRYSTAL STRUCTURE OF HUMAN PDGF-BB IN COMPLEX WITH A MODIFIED TITLE 2 NUCLEOTIDE APTAMER (SOMAMER SL5) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PLATELET-DERIVED GROWTH FACTOR SUBUNIT B; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PDGF-BB, UNP RESIDUES 82-109; COMPND 5 SYNONYM: PDGF SUBUNIT B, PDGF-2, PLATELET-DERIVED GROWTH FACTOR B COMPND 6 CHAIN, PLATELET-DERIVED GROWTH FACTOR BETA POLYPEPTIDE, PROTO- COMPND 7 ONCOGENE C-SIS; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: SOMAMER SL5; COMPND 11 CHAIN: C; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: PDGFB, PDGF2, SIS; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 OTHER_DETAILS: SYNTHESIZED OLIGONUCLEOTIDE KEYWDS GROWTH FACTOR, SELEX, APTAMER, 5-MODIFIED DEOXYURIDINE, HORMONE-DNA KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR D.R.DAVIES,T.E.EDWARDS,N.JANJIC,A.D.GELINAS,C.ZHANG,T.C.JARVIS REVDAT 4 20-NOV-24 4HQU 1 REMARK REVDAT 3 20-SEP-23 4HQU 1 REMARK LINK REVDAT 2 19-DEC-12 4HQU 1 JRNL REVDAT 1 21-NOV-12 4HQU 0 JRNL AUTH D.R.DAVIES,A.D.GELINAS,C.ZHANG,J.C.ROHLOFF,J.D.CARTER, JRNL AUTH 2 D.O'CONNELL,S.M.WAUGH,S.K.WOLK,W.S.MAYFIELD,A.B.BURGIN, JRNL AUTH 3 T.E.EDWARDS,L.J.STEWART,L.GOLD,N.JANJIC,T.C.JARVIS JRNL TITL UNIQUE MOTIFS AND HYDROPHOBIC INTERACTIONS SHAPE THE BINDING JRNL TITL 2 OF MODIFIED DNA LIGANDS TO PROTEIN TARGETS. JRNL REF PROC.NATL.ACAD.SCI.USA V. 109 19971 2012 JRNL REFN ISSN 0027-8424 JRNL PMID 23139410 JRNL DOI 10.1073/PNAS.1213933109 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.27 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 15628 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) : 0.227 REMARK 3 R VALUE (WORKING SET) : 0.225 REMARK 3 FREE R VALUE : 0.262 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 786 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) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.26 REMARK 3 REFLECTION IN BIN (WORKING SET) : 954 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.82 REMARK 3 BIN R VALUE (WORKING SET) : 0.3290 REMARK 3 BIN FREE R VALUE SET COUNT : 51 REMARK 3 BIN FREE R VALUE : 0.3530 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 738 REMARK 3 NUCLEIC ACID ATOMS : 556 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 82 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 50.44 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 43.68 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.88000 REMARK 3 B22 (A**2) : 1.88000 REMARK 3 B33 (A**2) : -3.77000 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): 0.196 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.181 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.137 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.589 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.949 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.922 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1381 ; 0.007 ; 0.018 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1973 ; 1.882 ; 2.136 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 96 ; 5.751 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 32 ;40.739 ;22.813 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 135 ;13.821 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 9 ;19.888 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 197 ; 0.091 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 893 ; 0.007 ; 0.021 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 : 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 USED IF REMARK 4 REMARK 4 4HQU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-OCT-12. REMARK 100 THE DEPOSITION ID IS D_1000075805. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-AUG-11 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 6.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979176 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15629 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 19.270 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.8 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.04000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 25.3300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.26 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.1 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.57800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.400 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: CHAIN A OF 3MJG REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 65.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.57 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROPLEX D8: 0.1 M MAGNESIUM ACETATE, REMARK 280 0.1 M SODIUM CACODYLATE PH 6.5, 15% PEG 6000, VAPOR DIFFUSION, REMARK 280 TEMPERATURE 289K, VAPOR DIFFUSION, SITTING DROP, PH 6.50 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 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 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -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 -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 83.50500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 29.85500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 29.85500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 41.75250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 29.85500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 29.85500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 125.25750 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 29.85500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 29.85500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 41.75250 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 29.85500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 29.85500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 125.25750 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 83.50500 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 10160 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18010 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 SER A 1 REMARK 465 LEU A 2 REMARK 465 GLY A 3 REMARK 465 SER A 4 REMARK 465 LEU A 5 REMARK 465 THR A 6 REMARK 465 VAL A 102 REMARK 465 ALA A 103 REMARK 465 ALA A 104 REMARK 465 ALA A 105 REMARK 465 ARG A 106 REMARK 465 PRO A 107 REMARK 465 VAL A 108 REMARK 465 THR A 109 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 ILE A 7 CG1 CG2 CD1 REMARK 470 GLU A 15 CG CD OE1 OE2 REMARK 470 ARG A 32 CG CD NE CZ NH1 NH2 REMARK 470 ASN A 57 CG OD1 ND2 REMARK 470 LYS A 80 CG CD CE NZ REMARK 470 LYS A 81 CG CD CE NZ 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 ASN A 36 48.41 -75.87 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA C 101 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DC C 10 O2 REMARK 620 2 DC C 10 O4' 65.9 REMARK 620 3 DG C 22 O6 92.2 150.8 REMARK 620 4 HOH C 214 O 84.9 81.9 76.9 REMARK 620 5 HOH C 215 O 167.4 101.6 100.2 95.7 REMARK 620 6 HOH C 216 O 87.6 79.8 120.1 161.7 88.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG C 102 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH C 201 O REMARK 620 2 HOH C 202 O 179.5 REMARK 620 3 HOH C 203 O 90.7 89.6 REMARK 620 4 HOH C 204 O 89.6 90.1 179.5 REMARK 620 5 HOH C 205 O 89.4 91.0 87.9 91.8 REMARK 620 6 HOH C 206 O 90.0 89.7 92.1 88.2 179.3 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA C 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG C 102 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3MJG RELATED DB: PDB REMARK 900 PDGF-BB BOUND TO RECEPTOR REMARK 900 RELATED ID: 4HQX RELATED DB: PDB REMARK 900 PDGF-BB IN COMPLEX WITH A MODIFIED NUCLEOTIDE APTAMER (SOMAMER SL4) DBREF 4HQU A 1 109 UNP P01127 PDGFB_HUMAN 82 190 DBREF 4HQU C 1 24 PDB 4HQU 4HQU 1 24 SEQRES 1 A 109 SER LEU GLY SER LEU THR ILE ALA GLU PRO ALA MET ILE SEQRES 2 A 109 ALA GLU CYS LYS THR ARG THR GLU VAL PHE GLU ILE SER SEQRES 3 A 109 ARG ARG LEU ILE ASP ARG THR ASN ALA ASN PHE LEU VAL SEQRES 4 A 109 TRP PRO PRO CYS VAL GLU VAL GLN ARG CYS SER GLY CYS SEQRES 5 A 109 CYS ASN ASN ARG ASN VAL GLN CYS ARG PRO THR GLN VAL SEQRES 6 A 109 GLN LEU ARG PRO VAL GLN VAL ARG LYS ILE GLU ILE VAL SEQRES 7 A 109 ARG LYS LYS PRO ILE PHE LYS LYS ALA THR VAL THR LEU SEQRES 8 A 109 GLU ASP HIS LEU ALA CYS LYS CYS GLU THR VAL ALA ALA SEQRES 9 A 109 ALA ARG PRO VAL THR SEQRES 1 C 24 DUZ DUZ A2M DC PE6 DG DUZ DUZ DA DC A2M DC DG SEQRES 2 C 24 DC DG DUZ UPE 18Q DA DUZ A2M DG DC 18M MODRES 4HQU DUZ C 1 DU MODRES 4HQU DUZ C 2 DU MODRES 4HQU A2M C 3 A MODRES 4HQU DUZ C 7 DU MODRES 4HQU DUZ C 8 DU MODRES 4HQU A2M C 11 A MODRES 4HQU DUZ C 16 DU MODRES 4HQU UPE C 17 DU MODRES 4HQU 18Q C 18 DU MODRES 4HQU DUZ C 20 DU MODRES 4HQU A2M C 21 A MODRES 4HQU 18M C 24 G HET DUZ C 1 26 HET DUZ C 2 29 HET A2M C 3 23 HET PE6 C 5 5 HET DUZ C 7 29 HET DUZ C 8 29 HET A2M C 11 23 HET DUZ C 16 29 HET UPE C 17 30 HET 18Q C 18 28 HET DUZ C 20 29 HET A2M C 21 23 HET 18M C 24 28 HET NA C 101 1 HET MG C 102 1 HETNAM DUZ 5-(BENZYLCARBAMOYL)-2'-DEOXYURIDINE 5'-(DIHYDROGEN HETNAM 2 DUZ PHOSPHATE) HETNAM A2M 2'-O-METHYLADENOSINE 5'-(DIHYDROGEN PHOSPHATE) HETNAM PE6 PHOSPHORYL-HEXAETHYLENE GLYCOL HETNAM UPE 2'-DEOXY-5-[(2-PHENYLETHYL)CARBAMOYL]URIDINE 5'- HETNAM 2 UPE (DIHYDROGEN PHOSPHATE) HETNAM 18Q 2'-DEOXY-5-[(THIOPHEN-2-YLMETHYL)CARBAMOYL]URIDINE 5'- HETNAM 2 18Q (DIHYDROGEN PHOSPHATE) HETNAM 18M 2'-O-METHYLGUANOSINE 3',5'-BIS(DIHYDROGEN PHOSPHATE) HETNAM NA SODIUM ION HETNAM MG MAGNESIUM ION FORMUL 2 DUZ 6(C17 H20 N3 O9 P) FORMUL 2 A2M 3(C11 H16 N5 O7 P) FORMUL 2 PE6 C12 H27 O10 P FORMUL 2 UPE C18 H22 N3 O9 P FORMUL 2 18Q C15 H18 N3 O9 P S FORMUL 2 18M C11 H17 N5 O11 P2 FORMUL 3 NA NA 1+ FORMUL 4 MG MG 2+ FORMUL 5 HOH *82(H2 O) HELIX 1 1 SER A 26 ASP A 31 1 6 SHEET 1 A 2 LYS A 17 GLU A 24 0 SHEET 2 A 2 CYS A 43 SER A 50 -1 O VAL A 44 N PHE A 23 SHEET 1 B 3 PHE A 37 TRP A 40 0 SHEET 2 B 3 GLN A 59 VAL A 78 -1 O ARG A 73 N TRP A 40 SHEET 3 B 3 LYS A 81 GLU A 100 -1 O LEU A 91 N ARG A 68 SSBOND 1 CYS A 16 CYS A 60 1555 1555 2.06 SSBOND 2 CYS A 43 CYS A 52 1555 7555 2.22 SSBOND 3 CYS A 49 CYS A 97 1555 1555 2.04 SSBOND 4 CYS A 53 CYS A 99 1555 1555 2.07 LINK O3' DC C 4 P1 PE6 C 5 1555 1555 1.60 LINK O20 PE6 C 5 P DG C 6 1555 1555 1.49 LINK O3' DG C 6 P DUZ C 7 1555 1555 1.60 LINK O3' DC C 10 P A2M C 11 1555 1555 1.59 LINK O3' DG C 15 P DUZ C 16 1555 1555 1.58 LINK O3' DA C 19 P DUZ C 20 1555 1555 1.60 LINK O2 DC C 10 NA NA C 101 1555 1555 2.44 LINK O4' DC C 10 NA NA C 101 1555 1555 2.92 LINK O6 DG C 22 NA NA C 101 1555 1555 2.43 LINK NA NA C 101 O HOH C 214 1555 1555 2.66 LINK NA NA C 101 O HOH C 215 1555 1555 2.25 LINK NA NA C 101 O HOH C 216 1555 1555 2.19 LINK MG MG C 102 O HOH C 201 1555 1555 2.18 LINK MG MG C 102 O HOH C 202 1555 1555 2.18 LINK MG MG C 102 O HOH C 203 1555 1555 2.18 LINK MG MG C 102 O HOH C 204 1555 1555 2.18 LINK MG MG C 102 O HOH C 205 1555 1555 2.17 LINK MG MG C 102 O HOH C 206 1555 1555 2.17 CISPEP 1 TRP A 40 PRO A 41 0 0.14 SITE 1 AC1 5 DC C 10 DG C 22 HOH C 214 HOH C 215 SITE 2 AC1 5 HOH C 216 SITE 1 AC2 6 HOH C 201 HOH C 202 HOH C 203 HOH C 204 SITE 2 AC2 6 HOH C 205 HOH C 206 CRYST1 59.710 59.710 167.010 90.00 90.00 90.00 P 41 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 0.016748 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016748 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005988 0.00000 CONECT 63 415 CONECT 339 711 CONECT 361 726 CONECT 415 63 CONECT 711 339 CONECT 726 361 CONECT 744 745 751 752 CONECT 745 744 746 747 CONECT 746 745 CONECT 747 745 748 CONECT 748 747 749 750 CONECT 749 748 CONECT 750 748 751 754 CONECT 751 744 750 CONECT 752 744 753 767 CONECT 753 752 763 CONECT 754 750 755 756 CONECT 755 754 CONECT 756 754 757 CONECT 757 756 758 CONECT 758 757 759 765 CONECT 759 758 760 CONECT 760 759 761 CONECT 761 760 762 CONECT 762 761 765 CONECT 763 753 764 766 CONECT 764 763 CONECT 765 758 762 CONECT 766 763 767 768 CONECT 767 752 766 CONECT 768 766 769 CONECT 769 768 CONECT 770 796 797 798 CONECT 771 772 778 779 CONECT 772 771 773 774 CONECT 773 772 CONECT 774 772 775 CONECT 775 774 776 777 CONECT 776 775 CONECT 777 775 778 781 CONECT 778 771 777 CONECT 779 771 780 794 CONECT 780 779 790 CONECT 781 777 782 783 CONECT 782 781 CONECT 783 781 784 CONECT 784 783 785 CONECT 785 784 786 792 CONECT 786 785 787 CONECT 787 786 788 CONECT 788 787 789 CONECT 789 788 792 CONECT 790 780 791 793 CONECT 791 790 CONECT 792 785 789 CONECT 793 790 794 795 CONECT 794 779 793 CONECT 795 793 796 CONECT 796 770 795 CONECT 797 770 CONECT 798 770 CONECT 799 800 801 821 CONECT 800 799 CONECT 801 799 802 CONECT 802 801 803 CONECT 803 802 804 805 CONECT 804 803 809 CONECT 805 803 806 807 CONECT 806 805 CONECT 807 805 808 809 CONECT 808 807 810 CONECT 809 804 807 811 CONECT 810 808 CONECT 811 809 812 820 CONECT 812 811 813 CONECT 813 812 814 CONECT 814 813 815 820 CONECT 815 814 816 817 CONECT 816 815 CONECT 817 815 818 CONECT 818 817 819 CONECT 819 818 820 CONECT 820 811 814 819 CONECT 821 799 CONECT 830 842 CONECT 841 842 CONECT 842 830 841 843 844 CONECT 843 842 CONECT 844 842 CONECT 845 846 CONECT 846 845 CONECT 854 868 CONECT 868 854 894 895 896 CONECT 869 870 876 877 CONECT 870 869 871 872 CONECT 871 870 CONECT 872 870 873 CONECT 873 872 874 875 CONECT 874 873 CONECT 875 873 876 879 CONECT 876 869 875 CONECT 877 869 878 892 CONECT 878 877 888 CONECT 879 875 880 881 CONECT 880 879 CONECT 881 879 882 CONECT 882 881 883 CONECT 883 882 884 890 CONECT 884 883 885 CONECT 885 884 886 CONECT 886 885 887 CONECT 887 886 890 CONECT 888 878 889 891 CONECT 889 888 CONECT 890 883 887 CONECT 891 888 892 893 CONECT 892 877 891 CONECT 893 891 894 CONECT 894 868 893 CONECT 895 868 CONECT 896 868 CONECT 897 923 924 925 CONECT 898 899 905 906 CONECT 899 898 900 901 CONECT 900 899 CONECT 901 899 902 CONECT 902 901 903 904 CONECT 903 902 CONECT 904 902 905 908 CONECT 905 898 904 CONECT 906 898 907 921 CONECT 907 906 917 CONECT 908 904 909 910 CONECT 909 908 CONECT 910 908 911 CONECT 911 910 912 CONECT 912 911 913 919 CONECT 913 912 914 CONECT 914 913 915 CONECT 915 914 916 CONECT 916 915 919 CONECT 917 907 918 920 CONECT 918 917 CONECT 919 912 916 CONECT 920 917 921 922 CONECT 921 906 920 CONECT 922 920 923 CONECT 923 897 922 CONECT 924 897 CONECT 925 897 CONECT 953 1301 CONECT 955 966 CONECT 960 1301 CONECT 966 955 967 968 988 CONECT 967 966 CONECT 968 966 969 CONECT 969 968 970 CONECT 970 969 971 972 CONECT 971 970 976 CONECT 972 970 973 974 CONECT 973 972 CONECT 974 972 975 976 CONECT 975 974 977 CONECT 976 971 974 978 CONECT 977 975 CONECT 978 976 979 987 CONECT 979 978 980 CONECT 980 979 981 CONECT 981 980 982 987 CONECT 982 981 983 984 CONECT 983 982 CONECT 984 982 985 CONECT 985 984 986 CONECT 986 985 987 CONECT 987 978 981 986 CONECT 988 966 CONECT 1057 1071 CONECT 1071 1057 1097 1098 1099 CONECT 1072 1073 1079 1080 CONECT 1073 1072 1074 1075 CONECT 1074 1073 CONECT 1075 1073 1076 CONECT 1076 1075 1077 1078 CONECT 1077 1076 CONECT 1078 1076 1079 1082 CONECT 1079 1072 1078 CONECT 1080 1072 1081 1095 CONECT 1081 1080 1091 CONECT 1082 1078 1083 1084 CONECT 1083 1082 CONECT 1084 1082 1085 CONECT 1085 1084 1086 CONECT 1086 1085 1087 1093 CONECT 1087 1086 1088 CONECT 1088 1087 1089 CONECT 1089 1088 1090 CONECT 1090 1089 1093 CONECT 1091 1081 1092 1094 CONECT 1092 1091 CONECT 1093 1086 1090 CONECT 1094 1091 1095 1096 CONECT 1095 1080 1094 CONECT 1096 1094 1097 CONECT 1097 1071 1096 CONECT 1098 1071 CONECT 1099 1071 CONECT 1100 1127 1128 1129 CONECT 1101 1102 1108 1109 CONECT 1102 1101 1103 1104 CONECT 1103 1102 CONECT 1104 1102 1105 CONECT 1105 1104 1106 1107 CONECT 1106 1105 CONECT 1107 1105 1108 1111 CONECT 1108 1101 1107 CONECT 1109 1101 1110 1125 CONECT 1110 1109 1120 CONECT 1111 1107 1112 1113 CONECT 1112 1111 CONECT 1113 1111 1114 CONECT 1114 1113 1115 CONECT 1115 1114 1116 CONECT 1116 1115 1117 1123 CONECT 1117 1116 1118 CONECT 1118 1117 1119 CONECT 1119 1118 1122 CONECT 1120 1110 1121 1124 CONECT 1121 1120 CONECT 1122 1119 1123 CONECT 1123 1116 1122 CONECT 1124 1120 1125 1126 CONECT 1125 1109 1124 CONECT 1126 1124 1127 CONECT 1127 1100 1126 CONECT 1128 1100 CONECT 1129 1100 CONECT 1130 1155 1156 1157 CONECT 1131 1132 1138 1139 CONECT 1132 1131 1133 1134 CONECT 1133 1132 CONECT 1134 1132 1135 CONECT 1135 1134 1136 1137 CONECT 1136 1135 CONECT 1137 1135 1138 1141 CONECT 1138 1131 1137 CONECT 1139 1131 1140 1153 CONECT 1140 1139 1150 CONECT 1141 1137 1142 1143 CONECT 1142 1141 CONECT 1143 1141 1144 CONECT 1144 1143 1145 CONECT 1145 1144 1146 1149 CONECT 1146 1145 1147 CONECT 1147 1146 1148 CONECT 1148 1147 1149 CONECT 1149 1145 1148 CONECT 1150 1140 1151 1152 CONECT 1151 1150 CONECT 1152 1150 1153 1154 CONECT 1153 1139 1152 CONECT 1154 1152 1155 CONECT 1155 1130 1154 CONECT 1156 1130 CONECT 1157 1130 CONECT 1166 1179 CONECT 1179 1166 1205 1206 1207 CONECT 1180 1181 1187 1188 CONECT 1181 1180 1182 1183 CONECT 1182 1181 CONECT 1183 1181 1184 CONECT 1184 1183 1185 1186 CONECT 1185 1184 CONECT 1186 1184 1187 1190 CONECT 1187 1180 1186 CONECT 1188 1180 1189 1203 CONECT 1189 1188 1199 CONECT 1190 1186 1191 1192 CONECT 1191 1190 CONECT 1192 1190 1193 CONECT 1193 1192 1194 CONECT 1194 1193 1195 1201 CONECT 1195 1194 1196 CONECT 1196 1195 1197 CONECT 1197 1196 1198 CONECT 1198 1197 1201 CONECT 1199 1189 1200 1202 CONECT 1200 1199 CONECT 1201 1194 1198 CONECT 1202 1199 1203 1204 CONECT 1203 1188 1202 CONECT 1204 1202 1205 CONECT 1205 1179 1204 CONECT 1206 1179 CONECT 1207 1179 CONECT 1208 1209 1210 1230 CONECT 1209 1208 CONECT 1210 1208 1211 CONECT 1211 1210 1212 CONECT 1212 1211 1213 1214 CONECT 1213 1212 1218 CONECT 1214 1212 1215 1216 CONECT 1215 1214 CONECT 1216 1214 1217 1218 CONECT 1217 1216 1219 CONECT 1218 1213 1216 1220 CONECT 1219 1217 CONECT 1220 1218 1221 1229 CONECT 1221 1220 1222 CONECT 1222 1221 1223 CONECT 1223 1222 1224 1229 CONECT 1224 1223 1225 1226 CONECT 1225 1224 CONECT 1226 1224 1227 CONECT 1227 1226 1228 CONECT 1228 1227 1229 CONECT 1229 1220 1223 1228 CONECT 1230 1208 CONECT 1247 1301 CONECT 1272 1273 1298 1299 CONECT 1273 1272 1274 CONECT 1274 1273 1275 CONECT 1275 1274 1276 1277 CONECT 1276 1275 1281 CONECT 1277 1275 1278 1279 CONECT 1278 1277 1293 CONECT 1279 1277 1280 1281 CONECT 1280 1279 1297 CONECT 1281 1276 1279 1282 CONECT 1282 1281 1283 1292 CONECT 1283 1282 1284 CONECT 1284 1283 1285 CONECT 1285 1284 1286 1292 CONECT 1286 1285 1287 1288 CONECT 1287 1286 CONECT 1288 1286 1289 CONECT 1289 1288 1290 1291 CONECT 1290 1289 CONECT 1291 1289 1292 CONECT 1292 1282 1285 1291 CONECT 1293 1278 1294 1295 1296 CONECT 1294 1293 CONECT 1295 1293 CONECT 1296 1293 CONECT 1297 1280 CONECT 1298 1272 CONECT 1299 1272 CONECT 1301 953 960 1247 1362 CONECT 1301 1363 1364 CONECT 1302 1349 1350 1351 1352 CONECT 1302 1353 1354 CONECT 1349 1302 CONECT 1350 1302 CONECT 1351 1302 CONECT 1352 1302 CONECT 1353 1302 CONECT 1354 1302 CONECT 1362 1301 CONECT 1363 1301 CONECT 1364 1301 MASTER 350 0 15 1 5 0 4 6 1378 2 359 11 END