PDB entry 6om2

View 6om2 on RCSB PDB site
Description: crystal structure of atypical integrin alphav beta8 with protgf-beta1 ligand peptide
Deposited on 2019-04-17, released 2019-12-11
The last revision was dated 2020-07-29, with a file datestamp of 2020-07-04.
Experiment type: XRAY
Resolution: 2.77 Å
R-factor: N/A
AEROSPACI score: 0.23 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Integrin alpha-V
    Species: Homo sapiens [TaxId:9606]
    Gene: ITGAV, MSK8, VNRA, VTNR
    Database cross-references and differences (RAF-indexed):
    • Uniprot P06756 (0-594)
      • insertion (399)
      • engineered mutation (400)
      • expression tag (595-597)
  • Chain 'B':
    Compound: Integrin beta-8
    Species: Homo sapiens [TaxId:9606]
    Gene: ITGB8
    Database cross-references and differences (RAF-indexed):
    • Uniprot P26012
      • engineered mutation (258)
  • Chain 'C':
    Compound: Integrin alpha-V
    Species: Homo sapiens [TaxId:9606]
    Gene: ITGAV, MSK8, VNRA, VTNR
    Database cross-references and differences (RAF-indexed):
    • Uniprot P06756 (0-594)
      • insertion (399)
      • engineered mutation (400)
      • expression tag (595)
  • Chain 'D':
    Compound: Integrin beta-8
    Species: Homo sapiens [TaxId:9606]
    Gene: ITGB8
    Database cross-references and differences (RAF-indexed):
    • Uniprot P26012 (Start-420)
      • engineered mutation (258)
  • Chain 'E':
    Compound: proTGF-beta1 RGD peptide
    Species: HOMO SAPIENS, synthetic [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 6OM2 (0-End)
  • Chain 'F':
    Compound: proTGF-beta1 RGD peptide
    Species: HOMO SAPIENS, synthetic [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 6OM2
  • Heterogens: CA, NAG, PEG, MG, GLY, HOH

PDB Chain Sequences:
This PDB entry is not classified in SCOPe 2.08, so the chain sequences below are not included in the ASTRAL sequence sets.

  • Chain 'A':
    Sequence; same for both SEQRES and ATOM records:
    >6om2A (A:)
fnldvdspaeysgpegsyfgfavdffvpsassrmfllvgapkanttqpgiveggqvlkcd
wsstrrcqpiefdatgnrdyakddplefkshqwfgasvrskqdkilacaplyhwrtemkq
erepvgtcflqdgtktveyapcrsqdidadgqgfcqggfsidftkadrvllggpgsfywq
gqlisdqvaeivskydpnvysikynnqlatrtaqaifddsylgysvavgdfngdgiddfv
sgvpraartlgmvyiydgknmsslynftgeqmaayfgfsvaatdingddyadvfigaplf
mdrgsdgklqevgqvsvslqrasgdfqttklngfevfarfgsaiaplgdldqdgfndiai
aapyggedkkgivyifngrstglnavpsqilegqwaarsgcppsfgysmkgatdidkngy
pdlivgafgvdrailyrarpvitvnaglevypsilnqdnktcslpgtalkvscfnvrfcl
kadgkgvlprklnfqvellldklkqkgairralflysrspshsknmtisrgglmqceeli
aylrdesefrdkltpitifmeyrldyrtaadttglqpilnqftpanisrqahilltgg

  • Chain 'B':
    Sequence, based on SEQRES records:
    >6om2B (B:)
ednrcassnaascarclalgpecgwcvqedfisggsrsercdivsnliskgcsvdsieyp
svhviipteneintqvtpgevsiqlrpgaeanfmlkvhplkkypvdlyylvdvsasmhnn
ieklnsvgndlsrkmaffsrdfrlgfgsyvdktvspyisihperihnqcsdynldcmpph
gyihvlsltenitefekavhrqkisgnidtpeggfdamlqaavceshigwrkeakrlllv
mtdqtshlaldsklagivcpndgnchlknnvyvksttmehpslgqlseklidnninvifa
vqgkqfhwykdllpllpgtiageieskaanlnnlvveayqklisevkvqvenqvqgiyfn
itaicpdgsrkpgmegcrnvtsndevlfnvtvtmkkcdvtggknyaiikpigfnetakih
i

    Sequence, based on observed residues (ATOM records):
    >6om2B (B:)
intqvtpgnfmlkvhpvdlyylvdvsasmhnnieklnsndlsrkmaffsrdfrlgfgsyv
dktvspyisihperihnqcsdynldcmpphgyihvlsltenitefekavhrqkisgnidt
peggfdamlqaavceshigwrkeakrlllvmtdqtshlaldsklagivcpndgnchlknn
vyvksttmehpslgqlseklidnninvifavqgkqfhwykdllpllpgtiageieskaan
lnnlvveayqklisevkvqvenqvqgiyfnitaicpdmegcrnvsndevlfnvtvtmkny
iikpigfnak

  • Chain 'C':
    Sequence, based on SEQRES records:
    >6om2C (C:)
fnldvdspaeysgpegsyfgfavdffvpsassrmfllvgapkanttqpgiveggqvlkcd
wsstrrcqpiefdatgnrdyakddplefkshqwfgasvrskqdkilacaplyhwrtemkq
erepvgtcflqdgtktveyapcrsqdidadgqgfcqggfsidftkadrvllggpgsfywq
gqlisdqvaeivskydpnvysikynnqlatrtaqaifddsylgysvavgdfngdgiddfv
sgvpraartlgmvyiydgknmsslynftgeqmaayfgfsvaatdingddyadvfigaplf
mdrgsdgklqevgqvsvslqrasgdfqttklngfevfarfgsaiaplgdldqdgfndiai
aapyggedkkgivyifngrstglnavpsqilegqwaarsgcppsfgysmkgatdidkngy
pdlivgafgvdrailyrarpvitvnaglevypsilnqdnktcslpgtalkvscfnvrfcl
kadgkgvlprklnfqvellldklkqkgairralflysrspshsknmtisrgglmqceeli
aylrdesefrdkltpitifmeyrldyrtaadttglqpilnqftpanisrqahilltgg

    Sequence, based on observed residues (ATOM records):
    >6om2C (C:)
fnldvdspaeysgpegsyfgfavdffvpsassrmfllvgapkanttqpgiveggqvlkcd
wsstrrcqpiefdatgnrdyakddplefkshqwfgasvrskqdkilacaplyhwrtemkq
erepvgtcflqdgtktveyapcrsqdidadgqgfcqggfsidftkadrvllggpgsfywq
gqlisdqvaeivskydpnvysikynnqlatrtaqaifddsylgysvavgdfngdgiddfv
sgvpraartlgmvyiydgknmsslynftgeqmaayfgfsvaatdingddyadvfigaplf
mdrgsdgklqevgqvsvslqrasgdfqttklngfevfarfgsaiaplgdldqdgfndiai
aapyggedkkgivyifngrstglnavpsqilegqwaarsgcppsfgysmkgatdidkngy
pdlivgafgvdrailyrarpvitvnaglevypsilnqdnktcslpgtalkvscfnvrfcl
kadgkgvlprklnfqvellldklkqkgairralflysrspshsknmtisrgglmqceeli
aylrdesefrdkltpitifmeyrldyrtaadttglqpilnqftpanisrqahillt

  • Chain 'D':
    Sequence, based on SEQRES records:
    >6om2D (D:)
ednrcassnaascarclalgpecgwcvqedfisggsrsercdivsnliskgcsvdsieyp
svhviipteneintqvtpgevsiqlrpgaeanfmlkvhplkkypvdlyylvdvsasmhnn
ieklnsvgndlsrkmaffsrdfrlgfgsyvdktvspyisihperihnqcsdynldcmpph
gyihvlsltenitefekavhrqkisgnidtpeggfdamlqaavceshigwrkeakrlllv
mtdqtshlaldsklagivcpndgnchlknnvyvksttmehpslgqlseklidnninvifa
vqgkqfhwykdllpllpgtiageieskaanlnnlvveayqklisevkvqvenqvqgiyfn
itaicpdgsrkpgmegcrnvtsndevlfnvtvtmkkcdvtggknyaiikpigfnetakih
i

    Sequence, based on observed residues (ATOM records):
    >6om2D (D:)
neintqvtpgeanfmlkvhplkkypvdlyylvdvsasmhnnieklnsvgndlsrkmaffs
rdfrlgfgsyvdktvspyisihperihnqcsdynldcmpphgyihvlsltenitefekav
hrqkisgnidtpeggfdamlqaavceshigwrkeakrlllvmtdqtshlaldsklagivc
pndgnchlknnvyvksttmehpslgqlseklidnninvifavqgkqfhwykdllpllpgt
iageieskaanlnnlvveayqklisevkvqvenqvqgyfnitaicpdgsrkpgmegcrnv
sndevlfnvtvtmyaiikpigfnetakihi

  • Chain 'E':
    Sequence, based on SEQRES records:
    >6om2E (E:)
grrgdlatihg

    Sequence, based on observed residues (ATOM records):
    >6om2E (E:)
grrgdlatih

  • Chain 'F':
    Sequence, based on SEQRES records:
    >6om2F (F:)
grrgdlatihg

    Sequence, based on observed residues (ATOM records):
    >6om2F (F:)
rrgdlatih