PDB entry 5ibk

View 5ibk on RCSB PDB site
Description: Skp1-F-box in complex with a ubiquitin variant
Class: protein binding
Keywords: phage display, SCF inhibitors, Fbxw7, Fbxw11, ?-Trcp, ubiquitin, PROTEIN BINDING
Deposited on 2016-02-22, released 2016-03-30
The last revision prior to the SCOPe 2.07 freeze date was dated 2017-09-13, with a file datestamp of 2017-09-08.
Experiment type: XRAY
Resolution: 2.5 Å
R-factor: N/A
AEROSPACI score: 0.22 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: S-phase kinase-associated protein 1,S-phase kinase-associated protein 1
    Species: Homo sapiens [TaxId:9606]
    Gene: SKP1, EMC19, OCP2, SKP1A, TCEB1L
    Database cross-references and differences (RAF-indexed):
    • Uniprot P63208 (2-End)
      • expression tag (0-1)
      • linker (65)
    • Uniprot P63208 (69-End)
    Domains in SCOPe 2.07: d5ibka1, d5ibka2, d5ibka3
  • Chain 'B':
    Compound: F-box/WD repeat-containing protein 7
    Species: Homo sapiens [TaxId:9606]
    Gene: FBXW7, FBW7, FBX30, SEL10
    Database cross-references and differences (RAF-indexed):
  • Chain 'C':
    Compound: Polyubiquitin-B
    Species: Homo sapiens [TaxId:9606]
    Gene: UBB
    Database cross-references and differences (RAF-indexed):
    • Uniprot P0CG47 (2-77)
      • engineered mutation (3)
      • engineered mutation (11-15)
      • engineered mutation (45)
      • engineered mutation (49-50)
      • engineered mutation (52)
      • engineered mutation (65-66)
      • engineered mutation (71)
      • engineered mutation (75-76)
    Domains in SCOPe 2.07: d5ibkc_
  • Chain 'D':
    Compound: S-phase kinase-associated protein 1,S-phase kinase-associated protein 1
    Species: Homo sapiens [TaxId:9606]
    Gene: SKP1, EMC19, OCP2, SKP1A, TCEB1L
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d5ibkd1, d5ibkd2
  • Chain 'E':
    Compound: F-box/WD repeat-containing protein 7
    Species: Homo sapiens [TaxId:9606]
    Gene: FBXW7, FBW7, FBX30, SEL10
    Database cross-references and differences (RAF-indexed):
  • Chain 'F':
    Compound: Polyubiquitin-B
    Species: Homo sapiens [TaxId:9606]
    Gene: UBB
    Database cross-references and differences (RAF-indexed):
    • Uniprot P0CG47 (Start-77)
      • engineered mutation (3)
      • engineered mutation (11-15)
      • engineered mutation (45)
      • engineered mutation (49-50)
      • engineered mutation (52)
      • engineered mutation (65-66)
      • engineered mutation (71)
      • engineered mutation (75-76)
    Domains in SCOPe 2.07: d5ibkf_
  • Heterogens: HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download) 
    >5ibkA (A:)
gampsiklqssdgeifevdveiakqsvtiktmledlgmdpvplpnvnaailkkviqwcth
hkddpggsgtddipvwdqeflkvdqgtlfelilaanyldikglldvtcktvanmikgktp
eeirktfnikndfteeeeaqvrkenqwceek

    Sequence, based on observed residues (ATOM records): (download) 
    >5ibkA (A:)
gampsiklqssdgeifevdveiakqsvtiktmledlgmdpvplpnvnaailkkviqwcth
hkddpgtddipvwdqeflkvdqgtlfelilaanyldikglldvtcktvanmikgktpeei
rktfnikndfteeeeaqvrke

  • Chain 'B':
    No sequence available.

  • Chain 'C':
    Sequence, based on SEQRES records: (download) 
    >5ibkC (C:)
gsgsmqifvktgartaitlevepsdtienvkakiqdkegippdqqilifsrklledgrtl
sdynihrestlrlvlifr

    Sequence, based on observed residues (ATOM records): (download) 
    >5ibkC (C:)
gsmqifvktgartaitlevepsdtienvkakiqdkegippdqqilifsrklledgrtlsd
ynihrestlrlvlifr

  • Chain 'D':
    Sequence, based on SEQRES records: (download) 
    >5ibkD (D:)
gampsiklqssdgeifevdveiakqsvtiktmledlgmdpvplpnvnaailkkviqwcth
hkddpggsgtddipvwdqeflkvdqgtlfelilaanyldikglldvtcktvanmikgktp
eeirktfnikndfteeeeaqvrkenqwceek

    Sequence, based on observed residues (ATOM records): (download) 
    >5ibkD (D:)
mpsiklqssdgeifevdveiakqsvtiktmledlgmdpvplpnvnaailkkviqwcthhk
ddddipvwdqeflkvdqgtlfelilaanyldikglldvtcktvanmikgktpeeirktfn
ikndfteeeeaqvrkenqwc

  • Chain 'E':
    No sequence available.

  • Chain 'F':
    Sequence, based on SEQRES records: (download) 
    >5ibkF (F:)
gsgsmqifvktgartaitlevepsdtienvkakiqdkegippdqqilifsrklledgrtl
sdynihrestlrlvlifr

    Sequence, based on observed residues (ATOM records): (download) 
    >5ibkF (F:)
smqifvktgartaitlevepsdtienvkakiqdkegippdqqilifsrklledgrtlsdy
nihrestlrlvlifr