PDB entry 3p9w

View 3p9w on RCSB PDB site
Description: Crystal structure of an engineered human autonomous VH Domain in complex with VEGF
Class: signaling protein/immune system
Keywords: VH, Cystine Knot Cytokine, VEGF-R, SIGNALING PROTEIN, SIGNALING PROTEIN-IMMUNE SYSTEM complex
Deposited on 2010-10-18, released 2012-04-18
The last revision prior to the SCOPe 2.04 freeze date was dated 2013-06-19, with a file datestamp of 2013-06-14.
Experiment type: XRAY
Resolution: 2.41 Å
R-factor: 0.195
AEROSPACI score: 0.34 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Vascular Endothelial Growth Factor A
    Species: Homo sapiens [TaxId:9606]
    Gene: RP1-261G23.1-009, VEGF, VEGFA
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.04: d3p9wa_
  • Chain 'B':
    Compound: human VEGF
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 3P9W (0-122)
    Domains in SCOPe 2.04: d3p9wb_
  • Chain 'C':
    Compound: Vascular Endothelial Growth Factor A
    Species: Homo sapiens [TaxId:9606]
    Gene: RP1-261G23.1-009, VEGF, VEGFA
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.04: d3p9wc_
  • Chain 'D':
    Compound: human VEGF
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 3P9W
    Domains in SCOPe 2.04: d3p9wd_
  • Chain 'E':
    Compound: Vascular Endothelial Growth Factor A
    Species: Homo sapiens [TaxId:9606]
    Gene: RP1-261G23.1-009, VEGF, VEGFA
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.04: d3p9we_
  • Chain 'F':
    Compound: human VEGF
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 3P9W (Start-122)
    Domains in SCOPe 2.04: d3p9wf_
  • Chain 'G':
    Compound: Vascular Endothelial Growth Factor A
    Species: Homo sapiens [TaxId:9606]
    Gene: RP1-261G23.1-009, VEGF, VEGFA
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.04: d3p9wg_
  • Chain 'H':
    Compound: human VEGF
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 3P9W (Start-122)
    Domains in SCOPe 2.04: d3p9wh_
  • Heterogens: HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download) 
    >3p9wA (A:)
gsqnhhevvkfmdvyqrsychpietlvdifqeypdeieyifkpscvplmrcggccndegl
ecvpteesnitmqimrikphqgqhigemsflqhnkcecrpkkdrar

    Sequence, based on observed residues (ATOM records): (download) 
    >3p9wA (A:)
hevvkfmdvyqrsychpietlvdifqeypdeieyifkpscvplmrcggccndeglecvpt
eesnitmqimrikphqgqhigemsflqhnkcecrpk

  • Chain 'B':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >3p9wB (B:)
evqlvesggglvqpggslrlscaasgfnikdtyigwvrrapgkgeelvariyptngytry
adsvkgrftisadtskntaylqmnslraedtavyycyyhyygwhpgyglsyssgqgtlvt
vss

  • Chain 'C':
    Sequence, based on SEQRES records: (download) 
    >3p9wC (C:)
gsqnhhevvkfmdvyqrsychpietlvdifqeypdeieyifkpscvplmrcggccndegl
ecvpteesnitmqimrikphqgqhigemsflqhnkcecrpkkdrar

    Sequence, based on observed residues (ATOM records): (download) 
    >3p9wC (C:)
hevvkfmdvyqrsychpietlvdifqeypdeieyifkpscvplmrcggccndeglecvpt
eesnitmqimrikphqgqhigemsflqhnkcecrpkk

  • Chain 'D':
    Sequence, based on SEQRES records: (download) 
    >3p9wD (D:)
evqlvesggglvqpggslrlscaasgfnikdtyigwvrrapgkgeelvariyptngytry
adsvkgrftisadtskntaylqmnslraedtavyycyyhyygwhpgyglsyssgqgtlvt
vss

    Sequence, based on observed residues (ATOM records): (download) 
    >3p9wD (D:)
vqlvesggglvqpggslrlscaasgfnikdtyigwvrrapgkgeelvariyptngytrya
dsvkgrftisadtskntaylqmnslraedtavyycyyhyygwhpgyglsyssgqgtlvtv
s

  • Chain 'E':
    Sequence, based on SEQRES records: (download) 
    >3p9wE (E:)
gsqnhhevvkfmdvyqrsychpietlvdifqeypdeieyifkpscvplmrcggccndegl
ecvpteesnitmqimrikphqgqhigemsflqhnkcecrpkkdrar

    Sequence, based on observed residues (ATOM records): (download) 
    >3p9wE (E:)
hevvkfmdvyqrsychpietlvdifqeypdeieyifkpscvplmrcggccndeglecvpt
eesnitmqimrikphqgqhigemsflqhnkcecrpkk

  • Chain 'F':
    Sequence, based on SEQRES records: (download) 
    >3p9wF (F:)
evqlvesggglvqpggslrlscaasgfnikdtyigwvrrapgkgeelvariyptngytry
adsvkgrftisadtskntaylqmnslraedtavyycyyhyygwhpgyglsyssgqgtlvt
vss

    Sequence, based on observed residues (ATOM records): (download) 
    >3p9wF (F:)
vqlvesggglvqpggslrlscaasgfnikdtyigwvrrapgkgeelvariyptngytrya
dsvkgrftisadtskntaylqmnslraedtavyycyyhyygwhpgyglsyssgqgtlvtv
ss

  • Chain 'G':
    Sequence, based on SEQRES records: (download) 
    >3p9wG (G:)
gsqnhhevvkfmdvyqrsychpietlvdifqeypdeieyifkpscvplmrcggccndegl
ecvpteesnitmqimrikphqgqhigemsflqhnkcecrpkkdrar

    Sequence, based on observed residues (ATOM records): (download) 
    >3p9wG (G:)
hhevvkfmdvyqrsychpietlvdifqeypdeieyifkpscvplmrcggccndeglecvp
teesnitmqimrikphqgqhigemsflqhnkcecrpk

  • Chain 'H':
    Sequence, based on SEQRES records: (download) 
    >3p9wH (H:)
evqlvesggglvqpggslrlscaasgfnikdtyigwvrrapgkgeelvariyptngytry
adsvkgrftisadtskntaylqmnslraedtavyycyyhyygwhpgyglsyssgqgtlvt
vss

    Sequence, based on observed residues (ATOM records): (download) 
    >3p9wH (H:)
vqlvesggglvqpggslrlscaasgfnikdtyigwvrrapgkgeelvariyptngytrya
dsvkgrftisadtskntaylqmnslraedtavyycyyhyygwhpgyglsyssgqgtlvtv
ss