MolNFT v1 · #65979 · protein
Crystal structure of TRAF6 in complex with UBC13 in the C2 space group
3HCU · TNF receptor-associated factor 6: “Crystal structure of TRAF6 in complex with UBC13 in the C2 space group”. X-ray diffraction, 1 ligand (ZN), 5 pockets (best druggability 0.73). MolNFT v1 #65979 on GenesisL1: 3D structure, binding…
- PDB
- 3HCU
- Type
- protein
- Length
- 509 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TNF receptor-associated factor 6; Ubiquitin-conjugating enzyme E2 N
- EC
- 6.3.2.19
- UniProt
- Q9Y4K3, P61088
- Ligands
- ZN
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 31% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TNF receptor-associated factor 6 | protein | 106 | 28% helix, 19% strand | Q9Y4K3 |
| B | Ubiquitin-conjugating enzyme E2 N (EC 6.3.2.19) | protein | 150 | 35% helix, 20% strand | P61088 |
| C | TNF receptor-associated factor 6 | protein | 104 | 24% helix, 13% strand | Q9Y4K3 |
| D | Ubiquitin-conjugating enzyme E2 N (EC 6.3.2.19) | protein | 149 | 35% helix, 20% strand | P61088 |
Ligands and binding sites
- ZN · Zinc ion · metal · 6 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 896 | 0.73 | 0.77 | 93 | empty |
| 2 | 89 | 0.39 | 0.76 | 16 | empty |
| 3 | 102 | 0.37 | 0.75 | 16 | empty |
| 4 | 85 | 0.35 | 0.75 | 20 | empty |
| 5 | 56 | 0.32 | 0.77 | 17 | empty |
Interfaces
4 interfaces between chains.
- B–D · 702 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 588 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 574 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 78 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3HCU · Crystal structure of TRAF6 in complex with Ubc13 in the C2 space group · the same entry in another collection · chain D against D, TM-score 1.00
- Q9Y4K3 · AlphaFold monomer V2.0 prediction for TNF receptor-associated factor 6 (Q9Y4K3) · a predicted model of the same protein · chain C against A, TM-score 0.96
- P61088 · AlphaFold monomer V2.0 prediction for ubiquitin-conjugating enzyme E2 N (P61088) · a predicted model of the same protein · chain B against A, TM-score 0.95
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 Q9Y4K3
- Every structure of UniProt P61088
- Elsewhere: RCSB PDB 3HCU · PDBe 3HCU · UniProt Q9Y4K3 · UniProt P61088
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