Research workbench
Structure of a TRAF6-UBC13~UB complex
Analyse Structure of a TRAF6-UBC13~UB complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VO0
- Type
- protein
- Length
- 712 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TNF receptor-associated factor 6; Ubiquitin-conjugating enzyme E2 N; Ubiquitin
- EC
- 2.3.2.27, 2.3.2.23
- UniProt
- P61088, P0CG47
- Ligands
- ZN, K
- Pockets
- 10 · best druggability 0.61
Structure
x-ray diffraction · 5 distinct chains · 29% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TNF receptor-associated factor 6 (EC 2.3.2.27) | protein | 104 | 28% helix, 19% strand | — |
| B | Ubiquitin-conjugating enzyme E2 N (EC 2.3.2.23) | protein | 148 | 36% helix, 18% strand | P61088 |
| C, F | Ubiquitin | protein | 76 | 24% helix, 33% strand | P0CG47 |
| D | TNF receptor-associated factor 6 (EC 2.3.2.27) | protein | 159 | 24% helix, 20% strand | — |
| E | Ubiquitin-conjugating enzyme E2 N (EC 2.3.2.23) | protein | 149 | 33% helix, 17% strand | P61088 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 256 | 0.61 | 0.80 | 29 | empty |
| 2 | 57 | 0.56 | 0.89 | 18 | empty |
| 3 | 176 | 0.56 | 0.80 | 32 | empty |
| 4 | 75 | 0.44 | 0.81 | 15 | empty |
| 5 | 89 | 0.40 | 0.77 | 17 | empty |
Interfaces
9 interfaces between chains.
- B–C · 956 Ų buried · 14 hydrogen bonds · protein-protein
- E–F · 880 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 587 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 576 Ų buried · 8 hydrogen bonds · protein-protein
- D–E · 547 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 isopeptide (isopeptide).
Compared structures
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P61088
- Every structure of UniProt P0CG47
- Elsewhere: RCSB PDB 5VO0 · PDBe 5VO0 · UniProt P61088 · UniProt P0CG47
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