5D0K: UbE2D2:RNF165:Ub complex
Structure of UbE2D2:RNF165:Ub complex. Determined by X-ray diffraction at 2.65 Å resolution. Released 9 Dec 2015.
- Method
- X-ray diffraction
- Resolution
- 2.65 Å
- Organism
- Homo sapiens
- Chains
- 12
- Atoms
- 9,395
- Mol. weight
- 144.85 kDa
- Ligands
- ZN
- Released
- 9 Dec 2015
Explore 5D0K in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
5D0K contains 61 α-helices and 88 β-strands across 12 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.
Chains A, G and J: 8 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 1-15 | 15 | |
| α-helix | 17-18 | 2 | |
| β-strand | 21-26 | 6 | 1 |
| β-strand | 29-38 | 10 | 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 | 75 | 1 | 2 |
| β-strand | 78 | 1 | 2 |
| β-strand | 83 | 1 | 1 |
| β-strand | 84 | 1 | 2 |
| α-helix | 87-89 | 3 | |
| α-helix | 99-111 | 13 | |
| α-helix | 121-129 | 9 | |
| α-helix | 131-145 | 15 | |
Chains B, H and K: 4 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-6 | 5 | 21 |
| β-strand | 12-16 | 5 | 21 |
| β-strand | 22 | 1 | 22 |
| α-helix | 23-34 | 12 | |
| α-helix | 38-40 | 3 | |
| β-strand | 41-45 | 5 | 21 |
| β-strand | 48-49 | 2 | 21 |
| α-helix | 50-51 | 2 | |
| β-strand | 55 | 1 | 22 |
| α-helix | 57-59 | 3 | |
| β-strand | 66-71 | 6 | 21 |
Chain C: 4 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 258-264 | 7 | |
| β-strand | 266-269 | 4 | 3 |
| β-strand | 293 | 1 | 4 |
| α-helix | 299 | 1 | |
| β-strand | 300 | 1 | 4 |
| α-helix | 301 | 1 | |
| β-strand | 306-309 | 4 | 3 |
| β-strand | 315-317 | 3 | 3 |
| α-helix | 318-325 | 8 | |
| β-strand | 330 | 1 | 5 |
| β-strand | 337 | 1 | 5 |
Chain D: 8 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 1-15 | 15 | |
| α-helix | 17-18 | 2 | |
| β-strand | 21-26 | 6 | 6 |
| β-strand | 29-38 | 10 | 6 |
| α-helix | 39-40 | 2 | |
| β-strand | 49-55 | 7 | 6 |
| α-helix | 64-65 | 2 | |
| β-strand | 66-69 | 4 | 6 |
| β-strand | 75 | 1 | 7 |
| β-strand | 78 | 1 | 7 |
| β-strand | 83 | 1 | 6 |
| β-strand | 84 | 1 | 7 |
| α-helix | 87-89 | 3 | |
| α-helix | 99-111 | 13 | |
| α-helix | 121-129 | 9 | |
| α-helix | 131-146 | 16 | |
Chain E: 5 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-6 | 5 | 23 |
| β-strand | 12-16 | 5 | 23 |
| β-strand | 22 | 1 | 24 |
| α-helix | 23-34 | 12 | |
| α-helix | 38-40 | 3 | |
| β-strand | 41-45 | 5 | 23 |
| β-strand | 48-49 | 2 | 23 |
| α-helix | 50-51 | 2 | |
| β-strand | 55 | 1 | 24 |
| α-helix | 57-59 | 3 | |
| β-strand | 66-71 | 6 | 23 |
| α-helix | 72-73 | 2 | |
Chain F: 4 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 259-263 | 5 | |
| β-strand | 266-269 | 4 | 8 |
| β-strand | 293 | 1 | 9 |
| α-helix | 299 | 1 | |
| β-strand | 300 | 1 | 9 |
| α-helix | 301 | 1 | |
| β-strand | 306-309 | 4 | 8 |
| β-strand | 315-317 | 3 | 8 |
| α-helix | 318-325 | 8 | |
| β-strand | 330 | 1 | 10 |
| β-strand | 337 | 1 | 10 |
Chains I and L: 2 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 259-264 | 6 | |
| β-strand | 266-269 | 4 | 13 |
| β-strand | 293 | 1 | 14 |
| β-strand | 300 | 1 | 14 |
| β-strand | 306-309 | 4 | 13 |
| β-strand | 315-317 | 3 | 13 |
| α-helix | 318-325 | 8 | |
| β-strand | 330 | 1 | 15 |
| β-strand | 337 | 1 | 15 |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Ubiquitin-conjugating enzyme E2 D2 | A, D, G, J | protein | 152 | Homo sapiens | P62837 (AlphaFold model) |
| RING finger protein 165 | C, F, I, L | protein | 92 | Homo sapiens | Q6ZSG1 (AlphaFold model) |
| Polyubiquitin-B | B, E, H, K | protein | 76 | Homo sapiens | P0CG47 (AlphaFold model) |
Sequence of entity 1 (A, D, G, J), FASTA
>5D0K_1 Ubiquitin-conjugating enzyme E2 D2 (chains A, D, G, J)
GPLGSMALKRIHKELNDLARDPPAQSSAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIH
FPTDYPFKPPKVAFTTRIYHPNINSNGSIKLDILRSQWSPALTISKVLLSISSLLSDPNP
DDPLVPEIARIYKTDREKYNRIAREWTQKYAM
Sequence of entity 2 (C, F, I, L), FASTA
>5D0K_2 RING finger protein 165 (chains C, F, I, L)
GPLGSGAVQNTIERFTFPHKYKKGKGKKDEGEESDTDEKCTICLSMLEDGEDVRRLPCMH
LFHQLCVDQWLAMSKKCPICRVDIETQLGADS
Sequence of entity 3 (B, E, H, K), FASTA
>5D0K_3 Polyubiquitin-B (chains B, E, H, K)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 8 |
Primary citation
Secondary ubiquitin-RING docking enhances Arkadia and Ark2C E3 ligase activity. Wright, J.D., Mace, P.D., Day, C.L. Nat Struct Mol Biol (2016) 23:45-52. DOI 10.1038/nsmb.3142 · 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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