HEADER HORMONE/DNA 26-OCT-12 4HQX TITLE CRYSTAL STRUCTURE OF HUMAN PDGF-BB IN COMPLEX WITH A MODIFIED TITLE 2 NUCLEOTIDE APTAMER (SOMAMER SL4) 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 SL4; 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 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 SYNTHETIC: YES; SOURCE 9 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 3 20-SEP-23 4HQX 1 REMARK LINK REVDAT 2 19-DEC-12 4HQX 1 JRNL REVDAT 1 21-NOV-12 4HQX 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. 2.30 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.68 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 13750 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) : 0.241 REMARK 3 R VALUE (WORKING SET) : 0.239 REMARK 3 FREE R VALUE : 0.279 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 679 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) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.36 REMARK 3 REFLECTION IN BIN (WORKING SET) : 824 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.19 REMARK 3 BIN R VALUE (WORKING SET) : 0.3660 REMARK 3 BIN FREE R VALUE SET COUNT : 45 REMARK 3 BIN FREE R VALUE : 0.5260 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 738 REMARK 3 NUCLEIC ACID ATOMS : 553 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 58 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 50.08 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.86 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.33000 REMARK 3 B22 (A**2) : 2.33000 REMARK 3 B33 (A**2) : -4.66000 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): 0.238 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.212 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.183 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.240 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.939 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.920 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1377 ; 0.007 ; 0.018 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1968 ; 2.005 ; 2.135 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 96 ; 6.101 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 32 ;42.582 ;22.813 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 135 ;14.965 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 9 ;25.856 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 198 ; 0.100 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 886 ; 0.006 ; 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 4HQX 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_1000075808. 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 : 4.50 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 : 13750 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 19.675 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.06400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.2900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.36 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.4 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.57200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.600 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 (%): 66.57 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.68 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROPLEX E1: 0.1 M MAGNESIUM ACETATE, REMARK 280 0.1 M SODIUM ACETATE PH 4.5, 8% PEG 8000, VAPOR DIFFUSION, REMARK 280 TEMPERATURE 289K, VAPOR DIFFUSION, SITTING DROP, PH 4.50 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 84.08000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 29.71500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 29.71500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 42.04000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 29.71500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 29.71500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 126.12000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 29.71500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 29.71500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 42.04000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 29.71500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 29.71500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 126.12000 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 84.08000 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: 10210 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18040 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.0 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 84.08000 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 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 ARG A 32 CG CD NE CZ NH1 NH2 REMARK 470 ASN A 57 CG OD1 ND2 REMARK 470 GLN A 59 CG CD OE1 NE2 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: 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 A2M C 3 C3' - O3' - P ANGL. DEV. = 8.3 DEGREES REMARK 500 DG C 6 C3' - O3' - P ANGL. DEV. = 8.2 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 ASN A 36 46.26 -79.34 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 96.3 151.6 REMARK 620 4 HOH C 210 O 80.9 77.7 77.6 REMARK 620 5 HOH C 211 O 89.4 70.7 133.9 148.2 REMARK 620 N 1 2 3 4 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 179.7 REMARK 620 3 HOH C 203 O 91.5 88.7 REMARK 620 4 HOH C 204 O 88.7 91.1 179.1 REMARK 620 5 HOH C 205 O 89.9 90.3 88.6 90.4 REMARK 620 6 HOH C 206 O 90.3 89.5 91.1 89.8 179.7 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 RECEPTOR COMPLEX REMARK 900 RELATED ID: 4HQU RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN PDGF-BB IN COMPLEX WITH A MODIFIED REMARK 900 NUCLEOTIDE APTAMER (SOMAMER SL5) DBREF 4HQX A 1 102 UNP P01127 PDGFB_HUMAN 82 183 DBREF 4HQX C 1 24 PDB 4HQX 4HQX 1 24 SEQRES 1 A 102 SER LEU GLY SER LEU THR ILE ALA GLU PRO ALA MET ILE SEQRES 2 A 102 ALA GLU CYS LYS THR ARG THR GLU VAL PHE GLU ILE SER SEQRES 3 A 102 ARG ARG LEU ILE ASP ARG THR ASN ALA ASN PHE LEU VAL SEQRES 4 A 102 TRP PRO PRO CYS VAL GLU VAL GLN ARG CYS SER GLY CYS SEQRES 5 A 102 CYS ASN ASN ARG ASN VAL GLN CYS ARG PRO THR GLN VAL SEQRES 6 A 102 GLN LEU ARG PRO VAL GLN VAL ARG LYS ILE GLU ILE VAL SEQRES 7 A 102 ARG LYS LYS PRO ILE PHE LYS LYS ALA THR VAL THR LEU SEQRES 8 A 102 GLU ASP HIS LEU ALA CYS LYS CYS GLU THR VAL SEQRES 1 C 24 DUZ DUZ A2M DC PE6 DG DUZ UBI DA DC A2M DC DG SEQRES 2 C 24 DC DG DUZ UPE 18Q DA DUZ A2M DG DC 18M MODRES 4HQX DUZ C 1 DU MODRES 4HQX DUZ C 2 DU MODRES 4HQX A2M C 3 A MODRES 4HQX DUZ C 7 DU MODRES 4HQX UBI C 8 DU MODRES 4HQX A2M C 11 A MODRES 4HQX DUZ C 16 DU MODRES 4HQX UPE C 17 DU MODRES 4HQX 18Q C 18 DU MODRES 4HQX DUZ C 20 DU MODRES 4HQX A2M C 21 A MODRES 4HQX 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 UBI C 8 26 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 UBI 2'-DEOXY-5-[(2-METHYLPROPYL)CARBAMOYL]URIDINE 5'- HETNAM 2 UBI (DIHYDROGEN PHOSPHATE) 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 5(C17 H20 N3 O9 P) FORMUL 2 A2M 3(C11 H16 N5 O7 P) FORMUL 2 PE6 C12 H27 O10 P FORMUL 2 UBI C14 H22 N3 O9 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 *58(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 46 N GLU A 21 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 2.04 SSBOND 2 CYS A 43 CYS A 52 1555 8555 2.17 SSBOND 3 CYS A 49 CYS A 97 1555 1555 2.05 SSBOND 4 CYS A 53 CYS A 99 1555 1555 2.04 LINK O3' DC C 4 P1 PE6 C 5 1555 1555 1.61 LINK O20 PE6 C 5 P DG C 6 1555 1555 1.49 LINK O3' DG C 6 P DUZ C 7 1555 1555 1.59 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 1.61 LINK O2 DC C 10 NA NA C 101 1555 1555 2.38 LINK O4' DC C 10 NA NA C 101 1555 1555 3.08 LINK O6 DG C 22 NA NA C 101 1555 1555 2.39 LINK NA NA C 101 O HOH C 210 1555 1555 2.58 LINK NA NA C 101 O HOH C 211 1555 1555 2.29 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 -1.18 SITE 1 AC1 5 DC C 10 DG C 15 DG C 22 HOH C 210 SITE 2 AC1 5 HOH C 211 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 59.430 59.430 168.160 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 0.016827 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016827 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005947 0.00000