4AUQ: BIRC7-UbcH5b-Ub complex
Structure of BIRC7-UbcH5b-Ub complex. Determined by X-ray diffraction at 2.18 Å resolution. Released 15 Aug 2012.
- Method
- X-ray diffraction
- Resolution
- 2.18 Å
- Organism
- HOMO SAPIENS
- Chains
- 6
- Atoms
- 4,389
- Mol. weight
- 65.34 kDa
- Ligands
- ZN
- Released
- 15 Aug 2012
Explore 4AUQ in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
4AUQ contains 27 α-helices and 46 β-strands across 6 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.
Chain A: 7 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-15 | 13 | |
| β-strand | 21-25 | 5 | 1 |
| β-strand | 32-38 | 7 | 1 |
| α-helix | 39-40 | 2 | |
| β-strand | 49-55 | 7 | 1 |
| α-helix | 64-65 | 2 | |
| β-strand | 66-69 | 4 | 1 |
| β-strand | 78 | 1 | 2 |
| β-strand | 83 | 1 | 1 |
| β-strand | 84 | 1 | 2 |
| β-strand | 86 | 1 | 3 |
| α-helix | 87-89 | 3 | |
| α-helix | 99-111 | 13 | |
| α-helix | 121-129 | 9 | |
| α-helix | 131-145 | 15 | |
Chain B: 3 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 243-249 | 7 | |
| β-strand | 251 | 1 | 4 |
| β-strand | 259 | 1 | 4 |
| α-helix | 260 | 1 | |
| β-strand | 262-265 | 4 | 5 |
| β-strand | 270-271 | 2 | 5 |
| α-helix | 276-278 | 3 | |
| β-strand | 281 | 1 | 6 |
| β-strand | 288 | 1 | 6 |
| β-strand | 291-294 | 4 | 5 |
| β-strand | 296 | 1 | 7 |
Chain C: 4 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 1-6 | 6 | 8 |
| β-strand | 12-17 | 6 | 8 |
| β-strand | 22 | 1 | 9 |
| α-helix | 23-34 | 12 | |
| α-helix | 38-40 | 3 | |
| β-strand | 41-45 | 5 | 8 |
| β-strand | 48-49 | 2 | 8 |
| α-helix | 50-51 | 2 | |
| β-strand | 55 | 1 | 9 |
| α-helix | 57-59 | 3 | |
| β-strand | 66-71 | 6 | 8 |
| β-strand | 75 | 1 | 3 |
Chain D: 8 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-15 | 13 | |
| α-helix | 17-18 | 2 | |
| β-strand | 21-25 | 5 | 10 |
| β-strand | 32-38 | 7 | 10 |
| α-helix | 39-40 | 2 | |
| β-strand | 49-55 | 7 | 10 |
| α-helix | 64-65 | 2 | |
| β-strand | 66-69 | 4 | 10 |
| β-strand | 78 | 1 | 11 |
| β-strand | 83 | 1 | 10 |
| β-strand | 84 | 1 | 11 |
| α-helix | 87-89 | 3 | |
| α-helix | 99-111 | 13 | |
| α-helix | 121-129 | 9 | |
| α-helix | 131-145 | 15 | |
Chain E: 3 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 243-249 | 7 | |
| β-strand | 251 | 1 | 12 |
| β-strand | 259 | 1 | 12 |
| α-helix | 260 | 1 | |
| β-strand | 262-265 | 4 | 13 |
| β-strand | 269 | 1 | 7 |
| β-strand | 270-271 | 2 | 13 |
| α-helix | 276-278 | 3 | |
| β-strand | 281 | 1 | 14 |
| β-strand | 288 | 1 | 14 |
| β-strand | 291-294 | 4 | 13 |
Chain F: 2 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-6 | 4 | 15 |
| β-strand | 12-15 | 4 | 15 |
| β-strand | 22 | 1 | 16 |
| α-helix | 23-34 | 12 | |
| α-helix | 38-40 | 3 | |
| β-strand | 41-45 | 5 | 15 |
| β-strand | 48-50 | 3 | 15 |
| β-strand | 55 | 1 | 16 |
| β-strand | 66-71 | 6 | 15 |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Ubiquitin-conjugating enzyme E2 D2 | A, D | protein | 147 | HOMO SAPIENS | P62837 (AlphaFold model) |
| Baculoviral iap repeat-containing protein 7 | B, E | protein | 62 | HOMO SAPIENS | Q96CA5 (AlphaFold model) |
| Polyubiquitin-C | C, F | protein | 81 | HOMO SAPIENS | P0CG48 (AlphaFold model) |
Sequence of entity 1 (A, D), FASTA
>4AUQ_1 UBIQUITIN-CONJUGATING ENZYME E2 D2 (chains A, D)
MALKRIHKELNDLARDPPAQCRAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIHFPTDY
PFKPPKVAFTTRIYHPAINSNGSISLDILRSQWSPALTISKVLLSICSLLCDPNPDDPLV
PEIARIYKTDREKYNRIAREWTQKYAM
Sequence of entity 2 (B, E), FASTA
>4AUQ_2 BACULOVIRAL IAP REPEAT-CONTAINING PROTEIN 7 (chains B, E)
GSVEAQLRRLQEERTCKVCLDRAVSIVFVPCGHLVCAECAPGLQLCPICRAPVRSRVRTF
LS
Sequence of entity 3 (C, F), FASTA
>4AUQ_3 POLYUBIQUITIN-C (chains C, F)
GSGGSMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRT
LSDYNIQKESTLHLVLRLRGG
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 4 |
Primary citation
Birc7-E2 Ubiquitin Conjugate Structure Reveals the Mechanism of Ubiquitin Transfer by a Ring Dimer. Dou, H., Buetow, L., Sibbet, G.J. et al. Nat Struct Mol Biol (2012) 19:876. DOI 10.1038/NSMB.2379 · PubMed
Other PDB entries of the same protein (UniProt P62837 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 9GLS 1.25 Å, Crystal Structure of Human UBCH5B C85E
- 2ESK 1.36 Å, Human Ubiquitin-Conjugating Enzyme (E2) UbcH5b, wild-type
- 6SQO 1.41 Å, Crystal structure of human MDM2 RING domain homodimer bound to UbcH5B-Ub
- 2ESQ 1.44 Å, Human Ubiquitin-Conjugating Enzyme (E2) UbcH5b mutant Ser94Gly
- 2ESO 1.5 Å, Human Ubiquitin-Conjugating Enzyme (E2) UbcH5b mutant Ile37Ala
- 2ESP 1.52 Å, Human ubiquitin-conjugating enzyme (E2) UbcH5b mutant Ile88Ala
- 4V3L 1.53 Å, RNF38-UB-UbcH5B-Ub complex
- 7AI0 1.56 Å, Crystal structure of human MDM2-G443T RING domain homodimer bound to UbcH5B-Ub (Crystal…
- 5D1M 1.58 Å, Crystal Structure of UbcH5B in Complex with the RING-U5BR Fragment of AO7 (P199A)
- 3L1Y 1.6 Å, Crystal structure of human UBC4 E2 conjugating enzyme
- 5D1L 1.62 Å, Crystal Structure of UbcH5B in Complex with the RING-U5BR Fragment of AO7 (Y165A)
- 6HPR 1.7 Å, Crystal structure of cIAP1 RING domain bound to UbcH5B-Ub and a non-covalent Ub
Browse structure collections
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