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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN PDGF-BB IN COMPLEX WITH A MODIFIED NUCLEOTIDE APTAMER (SOMAMER SL5)
 
Authors :  D. R. Davies, T. E. Edwards, N. Janjic, A. D. Gelinas, C. Zhang, T. C. Jarv
Date :  26 Oct 12  (Deposition) - 21 Nov 12  (Release) - 19 Dec 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,C
Biol. Unit 1:  A,C  (2x)
Keywords :  Growth Factor, Selex, Aptamer, 5-Modified Deoxyuridine, Hormone-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. R. Davies, A. D. Gelinas, C. Zhang, J. C. Rohloff, J. D. Carter, D. O'Connell, S. M. Waugh, S. K. Wolk, W. S. Mayfield, A. B. Burgin, T. E. Edwards, L. J. Stewart, L. Gold, N. Janjic, T. C. Jarvis
Unique Motifs And Hydrophobic Interactions Shape The Bindin Of Modified Dna Ligands To Protein Targets.
Proc. Natl. Acad. Sci. Usa V. 109 19971 2012
PubMed-ID: 23139410  |  Reference-DOI: 10.1073/PNAS.1213933109

(-) Compounds

Molecule 1 - PLATELET-DERIVED GROWTH FACTOR SUBUNIT B
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: PDGF-BB, UNP RESIDUES 82-109
    Gene: PDGFB, PDGF2, SIS
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PDGF SUBUNIT B, PDGF-2, PLATELET-DERIVED GROWTH FACTOR B CHAIN, PLATELET-DERIVED GROWTH FACTOR BETA POLYPEPTIDE, PROTO- ONCOGENE C-SIS
 
Molecule 2 - SOMAMER SL5
    Chains: C
    Engineered: YES
    Other Details: SYNTHESIZED OLIGONUCLEOTIDE
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AC
Biological Unit 1 (2x): AC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (8, 15)

Asymmetric Unit (8, 15)
No.NameCountTypeFull Name
118M1Mod. Nucleotide2'-O-METHYLGUANOSINE 3',5'-BIS(DIHYDROGEN PHOSPHATE)
218Q1Mod. Nucleotide2'-DEOXY-5-[(THIOPHEN-2-YLMETHYL)CARBAMOYL]URIDINE 5'-(DIHYDROGEN PHOSPHATE)
3A2M3Mod. Nucleotide2'-O-METHYLADENOSINE 5'-(DIHYDROGEN PHOSPHATE)
4DUZ6Mod. Nucleotide5-(BENZYLCARBAMOYL)-2'-DEOXYURIDINE 5'-(DIHYDROGENPHOSPHATE)
5MG1Ligand/IonMAGNESIUM ION
6NA1Ligand/IonSODIUM ION
7PE61Mod. NucleotidePHOSPHORYL-HEXAETHYLENE GLYCOL
8UPE1Mod. Nucleotide2'-DEOXY-5-[(2-PHENYLETHYL)CARBAMOYL]URIDINE 5'-(DIHYDROGEN PHOSPHATE)
Biological Unit 1 (6, 26)
No.NameCountTypeFull Name
118M2Mod. Nucleotide2'-O-METHYLGUANOSINE 3',5'-BIS(DIHYDROGEN PHOSPHATE)
218Q2Mod. Nucleotide2'-DEOXY-5-[(THIOPHEN-2-YLMETHYL)CARBAMOYL]URIDINE 5'-(DIHYDROGEN PHOSPHATE)
3A2M6Mod. Nucleotide2'-O-METHYLADENOSINE 5'-(DIHYDROGEN PHOSPHATE)
4DUZ12Mod. Nucleotide5-(BENZYLCARBAMOYL)-2'-DEOXYURIDINE 5'-(DIHYDROGENPHOSPHATE)
5MG-1Ligand/IonMAGNESIUM ION
6NA-1Ligand/IonSODIUM ION
7PE62Mod. NucleotidePHOSPHORYL-HEXAETHYLENE GLYCOL
8UPE2Mod. Nucleotide2'-DEOXY-5-[(2-PHENYLETHYL)CARBAMOYL]URIDINE 5'-(DIHYDROGEN PHOSPHATE)

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREDC C:10 , DG C:22 , HOH C:214 , HOH C:215 , HOH C:216BINDING SITE FOR RESIDUE NA C 101
2AC2SOFTWAREHOH C:201 , HOH C:202 , HOH C:203 , HOH C:204 , HOH C:205 , HOH C:206BINDING SITE FOR RESIDUE MG C 102

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:16 -A:60
2A:43 -A:52
3A:49 -A:97
4A:53 -A:99

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Trp A:40 -Pro A:41

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4HQU)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4HQU)

(-) Exons   (0, 0)

(no "Exon" information available for 4HQU)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:95
                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeeeeee.hhhhhh.....eeee..eeeeeeee........eeeeeeeeeeeeeeeeeeee..eeeeeeeeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------- Transcript
                 4hqu A   7 IAEPAMIAECKTRTEVFEISRRLIDRTNANFLVWPPCVEVQRCSGCCNNRNVQCRPTQVQLRPVQVRKIEIVRKKPIFKKATVTLEDHLACKCET 101
                                    16        26        36        46        56        66        76        86        96     


Chain C from PDB  Type:DNA/RNA  Length:24
                                                        
                 4hqu C   1 xxaCxGxxACaCGCGxxxAxaGCg  24
                            ||| | ||10|    |||20|  |
                            1-DUZ ||  |    |18-18Q |
                             2-DUZ||  |    || 20-DUZ
                              3-A2M|  |    ||  21-A2M
                                5-PE6 |    ||     24-18M
                                  7-DUZ    ||       
                                   8-DUZ   ||       
                                     11-A2M||       
                                          16-DUZ    
                                           17-UPE
   Legend:   → Mismatch (orange background)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4HQU)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4HQU)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4HQU)

(-) Gene Ontology  (100, 100)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        PDGFB_HUMAN | P01127: 1pdg 3mjg 4hqx 4qci

(-) Related Entries Specified in the PDB File

3mjg PDGF-BB BOUND TO RECEPTOR
4hqx PDGF-BB IN COMPLEX WITH A MODIFIED NUCLEOTIDE APTAMER (SOMAMER SL4)