PDB entry 6byh

View 6byh on RCSB PDB site
Description: Ubiquitin Variant (UbV.Fl11.1) bound to a human Skp1-Fbl11 fragment complex.
Class: protein binding
Keywords: Ubiquitination, PROTEIN BINDING
Deposited on 2017-12-20, released 2018-07-18
The last revision prior to the SCOPe 2.07 freeze date was dated 2018-07-18, with a file datestamp of 2018-07-13.
Experiment type: XRAY
Resolution: 2.61 Å
R-factor: N/A
AEROSPACI score: 0.19 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: 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)
    Domains in SCOPe 2.07: d6byha1, d6byha2, d6byha3
  • Chain 'B':
    Compound: 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 (1)
    Domains in SCOPe 2.07: d6byhb1, d6byhb2, d6byhb3
  • Chain 'C':
    Compound: Polyubiquitin-B
    Species: Homo sapiens [TaxId:9606]
    Gene: UBB
    Database cross-references and differences (RAF-indexed):
    • Uniprot P0CG47 (2-81)
      • expression tag (0-1)
      • engineered mutation (10-13)
      • insertion (13)
      • insertion (13)
      • insertion (13)
      • insertion (13)
      • insertion (13)
      • insertion (13)
      • insertion (13)
      • engineered mutation (52)
      • engineered mutation (56-57)
      • engineered mutation (59)
      • engineered mutation (78)
      • engineered mutation (82-83)
    Domains in SCOPe 2.07: d6byhc1, d6byhc2
  • Chain 'D':
    Compound: Polyubiquitin-B
    Species: Homo sapiens [TaxId:9606]
    Gene: UBB
    Database cross-references and differences (RAF-indexed):
    • Uniprot P0CG47 (2-81)
      • expression tag (1)
      • engineered mutation (10-13)
      • insertion (13)
      • insertion (13)
      • insertion (13)
      • insertion (13)
      • insertion (13)
      • insertion (13)
      • insertion (13)
      • engineered mutation (52)
      • engineered mutation (56-57)
      • engineered mutation (59)
      • engineered mutation (78)
      • engineered mutation (82-85)
    Domains in SCOPe 2.07: d6byhd1, d6byhd2
  • Chain 'E':
    Compound: lysine-specific demethylase 2a
    Species: Homo sapiens [TaxId:9606]
    Gene: KDM2A, CXXC8, FBL7, FBXL11, JHDM1A, KIAA1004
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q9Y2K7 (2-End)
      • expression tag (1)
  • Chain 'F':
    Compound: lysine-specific demethylase 2a
    Species: Homo sapiens [TaxId:9606]
    Gene: KDM2A, CXXC8, FBL7, FBXL11, JHDM1A, KIAA1004
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q9Y2K7 (2-End)
      • expression tag (1)
  • Chain 'G':
    Compound: 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 (1)
    Domains in SCOPe 2.07: d6byhg1, d6byhg2, d6byhg3
  • Chain 'H':
    Compound: Polyubiquitin-B
    Species: Homo sapiens [TaxId:9606]
    Gene: UBB
    Database cross-references and differences (RAF-indexed):
    • Uniprot P0CG47 (2-81)
      • expression tag (1)
      • engineered mutation (10-13)
      • insertion (13)
      • insertion (13)
      • insertion (13)
      • insertion (13)
      • insertion (13)
      • insertion (13)
      • insertion (13)
      • engineered mutation (52)
      • engineered mutation (56-57)
      • engineered mutation (59)
      • engineered mutation (78)
      • engineered mutation (82-84)
    Domains in SCOPe 2.07: d6byhh1, d6byhh2
  • Chain 'I':
    Compound: lysine-specific demethylase 2a
    Species: Homo sapiens [TaxId:9606]
    Gene: KDM2A, CXXC8, FBL7, FBXL11, JHDM1A, KIAA1004
    Database cross-references and differences (RAF-indexed):
  • Heterogens: HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download) 
    >6byhA (A:)
gampsiklqssdgeifevdveiakqsvtiktmledlgmddegdddpvplpnvnaailkkv
iqwcthhkddppppeddenkekrtddipvwdqeflkvdqgtlfelilaanyldikglldv
tcktvanmikgktpeeirktfnikndfteeeeaqvrkenqwceek

    Sequence, based on observed residues (ATOM records): (download) 
    >6byhA (A:)
gampsiklqssdgeifevdveiakqsvtiktmleddddpvplpnvnaailkkviqwcthh
kddppenkekrtddipvwdqeflkvdqgtlfelilaanyldikglldvtcktvanmikgk
tpeeirktfnikndfteeeeaqvrk

  • Chain 'B':
    Sequence, based on SEQRES records: (download) 
    >6byhB (B:)
gampsiklqssdgeifevdveiakqsvtiktmledlgmddegdddpvplpnvnaailkkv
iqwcthhkddppppeddenkekrtddipvwdqeflkvdqgtlfelilaanyldikglldv
tcktvanmikgktpeeirktfnikndfteeeeaqvrkenqwceek

    Sequence, based on observed residues (ATOM records): (download) 
    >6byhB (B:)
ampsiklqssdgeifevdveiakqsvtiktmledldddpvplpnvnaailkkviqwcthh
kddpppekrtddipvwdqeflkvdqgtlfelilaanyldikglldvtcktvanmikgktp
eeirktfnikndfteeeeaqvrkenqwcee

  • Chain 'C':
    Sequence, based on SEQRES records: (download) 
    >6byhC (C:)
gsgmqifvktrhsykhglienstitlevepsdtienvkakiqdkegippdqqvlifsrkr
ledgrtlsdyniqkestlrlvlvfgrr

    Sequence, based on observed residues (ATOM records): (download) 
    >6byhC (C:)
gsgmqifvktrhsykhglienstitlevepsdtienvkakiqdkegippdqqvlifsrkr
ledgrtlsdyniqkestlrlvlvf

  • Chain 'D':
    Sequence, based on SEQRES records: (download) 
    >6byhD (D:)
gsgmqifvktrhsykhglienstitlevepsdtienvkakiqdkegippdqqvlifsrkr
ledgrtlsdyniqkestlrlvlvfgrr

    Sequence, based on observed residues (ATOM records): (download) 
    >6byhD (D:)
sgmqifvktrhsykhglienstitlevepsdtienvkakiqdkegippdqqvlifsrkrl
edgrtlsdyniqkestlrlvlvfgr

  • Chain 'E':
    No sequence available.

  • Chain 'F':
    No sequence available.

  • Chain 'G':
    Sequence, based on SEQRES records: (download) 
    >6byhG (G:)
gampsiklqssdgeifevdveiakqsvtiktmledlgmddegdddpvplpnvnaailkkv
iqwcthhkddppppeddenkekrtddipvwdqeflkvdqgtlfelilaanyldikglldv
tcktvanmikgktpeeirktfnikndfteeeeaqvrkenqwceek

    Sequence, based on observed residues (ATOM records): (download) 
    >6byhG (G:)
ampsiklqssdgeifevdveiakqsvtiktmledddpvplpnvnaailkkviqwcthhkd
dprtddipvwdqeflkvdqgtlfelilaanyldikglldvtcktvanmikgktpeeirkt
fniknd

  • Chain 'H':
    Sequence, based on SEQRES records: (download) 
    >6byhH (H:)
gsgmqifvktrhsykhglienstitlevepsdtienvkakiqdkegippdqqvlifsrkr
ledgrtlsdyniqkestlrlvlvfgrr

    Sequence, based on observed residues (ATOM records): (download) 
    >6byhH (H:)
sgmqifvktrhsykhglienstitlevepsdtienvkakiqdkegippdqqvlifsrkrl
edgrtlsdyniqkestlrlvlvfg

  • Chain 'I':
    No sequence available.