MolNFT v1 · #137420 · protein
Structure of a TRAF6-UBC13~UB complex
5VNZ · TNF receptor-associated factor 6: “Structure of a TRAF6-UBC13~UB complex”. X-ray diffraction, 1 ligand (ZN), 13 pockets (best druggability 0.61). MolNFT v1 #137420 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5VNZ
- Type
- protein
- Length
- 668 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
- Pockets
- 13 · best druggability 0.61
Structure
x-ray diffraction · 5 distinct chains · 32% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TNF receptor-associated factor 6 (EC 2.3.2.27) | protein | 108 | 30% helix, 17% strand | — |
| B | Ubiquitin-conjugating enzyme E2 N (EC 2.3.2.23) | protein | 148 | 36% helix, 18% strand | P61088 |
| C, F | Ubiquitin | protein | 76 | 25% helix, 30% strand | P0CG47 |
| D | TNF receptor-associated factor 6 (EC 2.3.2.27) | protein | 111 | 29% helix, 16% strand | — |
| E | Ubiquitin-conjugating enzyme E2 N (EC 2.3.2.23) | protein | 149 | 35% helix, 17% strand | P61088 |
Ligands and binding sites
- ZN · Zinc ion · metal · 6 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 169 | 0.61 | 0.83 | 17 | empty |
| 2 | 167 | 0.59 | 0.83 | 18 | empty |
| 3 | 99 | 0.48 | 0.81 | 15 | empty |
| 4 | 101 | 0.48 | 0.81 | 16 | empty |
| 5 | 53 | 0.40 | 0.82 | 14 | empty |
Interfaces
9 interfaces between chains.
- E–F · 868 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 830 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 590 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 582 Ų buried · 6 hydrogen bonds · protein-protein
- D–E · 573 Ų buried · 7 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 5VNZ · PDBe 5VNZ · UniProt P61088 · UniProt P0CG47
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