PDB entry 5d2m

View 5d2m on RCSB PDB site
Description: Complex between human SUMO2-RANGAP1, UBC9 and ZNF451
Class: Ligase,Protein Binding
Keywords: Complex, SUMO, E3 Ligase, Ligase, Protein Binding
Deposited on 2015-08-05, released 2015-11-04
The last revision prior to the SCOPe 2.08 freeze date was dated 2019-12-25, with a file datestamp of 2019-12-20.
Experiment type: XRAY
Resolution: 2.4 Å
R-factor: N/A
AEROSPACI score: 0.24 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: SUMO-conjugating enzyme UBC9
    Species: Homo sapiens [TaxId:9606]
    Gene: UBE2I, UBC9, UBCE9
    Database cross-references and differences (RAF-indexed):
    • Uniprot P63279 (3-End)
      • engineered mutation (16)
    Domains in SCOPe 2.08: d5d2ma_
  • Chain 'B':
    Compound: Small ubiquitin-related modifier 2
    Species: Homo sapiens [TaxId:9606]
    Gene: SUMO2, SMT3B, SMT3H2
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5d2mb_
  • Chain 'C':
    Compound: ran gtpase-activating protein 1
    Species: Homo sapiens [TaxId:9606]
    Gene: RANGAP1, KIAA1835, SD
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5d2mc_
  • Chain 'D':
    Compound: SUMO-conjugating enzyme UBC9
    Species: Homo sapiens [TaxId:9606]
    Gene: UBE2I, UBC9, UBCE9
    Database cross-references and differences (RAF-indexed):
    • Uniprot P63279 (3-End)
      • engineered mutation (16)
    Domains in SCOPe 2.08: d5d2md_
  • Chain 'E':
    Compound: Small ubiquitin-related modifier 2
    Species: Homo sapiens [TaxId:9606]
    Gene: SUMO2, SMT3B, SMT3H2
    Database cross-references and differences (RAF-indexed):
    • Uniprot P61956 (4-82)
      • expression tag (3)
    Domains in SCOPe 2.08: d5d2me1, d5d2me2
  • Chain 'F':
    Compound: ran gtpase-activating protein 1
    Species: Homo sapiens [TaxId:9606]
    Gene: RANGAP1, KIAA1835, SD
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5d2mf_
  • Chain 'G':
    Compound: Zinc finger protein 451
    Species: Homo sapiens [TaxId:9606]
    Gene: ZNF451, COASTER, KIAA0576, KIAA1702
    Database cross-references and differences (RAF-indexed):
  • Heterogens: EDO, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download) 
    >5d2mA (A:)
gshmsgialsrlaqerrawrkdhpfgfvavptknpdgtmnlmnwecaipgkkgtpweggl
fklrmlfkddypssppkckfepplfhpnvypsgtvclsileedkdwrpaitikqillgiq
ellnepniqdpaqaeaytiycqnrveyekrvraqakkfaps

    Sequence, based on observed residues (ATOM records): (download) 
    >5d2mA (A:)
msgialsrlaqerrawrkdhpfgfvavptknpdgtmnlmnwecaipgkkgtpwegglfkl
rmlfkddypssppkckfepplfhpnvypsgtvclsileedkdwrpaitikqillgiqell
nepniqdpaqaeaytiycqnrveyekrvraqakkfap

  • Chain 'B':
    Sequence, based on SEQRES records: (download) 
    >5d2mB (B:)
gshmndhinlkvagqdgsvvqfkikrhtplsklmkaycerqglsmrqirfrfdgqpinet
dtpaqlemededtidvfqqqtgg

    Sequence, based on observed residues (ATOM records): (download) 
    >5d2mB (B:)
inlkvagqdgsvvqfkikrhtplsklmkaycerqglsmrqirfrfdgqpinetdtpaqle
mededtidvfqqqtgg

  • Chain 'C':
    Sequence, based on SEQRES records: (download) 
    >5d2mC (C:)
sntgepapvlsspppadvstflafpspekllrlgpkssvliaqqtdtsdpekvvsaflkv
ssvfkdeatvrmavqdavdalmqkafnsssfnsntfltrllvhmgllksedkvkaianly
gplmalnhmvqqdyfpkalaplllafvtkpnsalescsfarhsllqtlykv

    Sequence, based on observed residues (ATOM records): (download) 
    >5d2mC (C:)
ppadvstflafpspekllrlgpkssvliaqqtdtsdpekvvsaflkvssvfkdeatvrma
vqdavdalmqkafnsssfnsntfltrllvhmgllksedkvkaianlygplmalnhmvqqd
yfpkalaplllafvtkpnsalescsfarhsllqtlykv

  • Chain 'D':
    Sequence, based on SEQRES records: (download) 
    >5d2mD (D:)
gshmsgialsrlaqerrawrkdhpfgfvavptknpdgtmnlmnwecaipgkkgtpweggl
fklrmlfkddypssppkckfepplfhpnvypsgtvclsileedkdwrpaitikqillgiq
ellnepniqdpaqaeaytiycqnrveyekrvraqakkfaps

    Sequence, based on observed residues (ATOM records): (download) 
    >5d2mD (D:)
msgialsrlaqerrawrkdhpfgfvavptknpdgtmnlmnwecaipgkkgtpwegglfkl
rmlfkddypssppkckfepplfhpnvypsgtvclsileedkdwrpaitikqillgiqell
nepniqdpaqaeaytiycqnrveyekrvraqakkfap

  • Chain 'E':
    Sequence, based on SEQRES records: (download) 
    >5d2mE (E:)
gshmndhinlkvagqdgsvvqfkikrhtplsklmkaycerqglsmrqirfrfdgqpinet
dtpaqlemededtidvfqqqtgg

    Sequence, based on observed residues (ATOM records): (download) 
    >5d2mE (E:)
mndhinlkvagqdgsvvqfkikrhtplsklmkaycerqglsmrqirfrfdgqpinetdtp
aqlemededtidvfqqqtgg

  • Chain 'F':
    Sequence, based on SEQRES records: (download) 
    >5d2mF (F:)
sntgepapvlsspppadvstflafpspekllrlgpkssvliaqqtdtsdpekvvsaflkv
ssvfkdeatvrmavqdavdalmqkafnsssfnsntfltrllvhmgllksedkvkaianly
gplmalnhmvqqdyfpkalaplllafvtkpnsalescsfarhsllqtlykv

    Sequence, based on observed residues (ATOM records): (download) 
    >5d2mF (F:)
padvstflafpspekllrlgpkssvliaqqtdtsdpekvvsaflkvssvfkdeatvrmav
qdavdalmqkafnsssfnsntfltrllvhmgllksedkvkaianlygplmalnhmvqqdy
fpkalaplllafvtkpnsalescsfarhsllqtlykv

  • Chain 'G':
    No sequence available.