MolNFT v1 · #65978 · protein
Crystal structure of TRAF6 in complex with UBC13 in the P1 space group
3HCT · TNF receptor-associated factor 6: “Crystal structure of TRAF6 in complex with UBC13 in the P1 space group”. X-ray diffraction, 1 ligand (ZN), 2 pockets (best druggability 0.46). MolNFT v1 #65978 on GenesisL1: 3D structure, binding…
- PDB
- 3HCT
- Type
- protein
- Length
- 252 residues
- Chains
- 2
- 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
- 2 · best druggability 0.46
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TNF receptor-associated factor 6 | protein | 104 | 30% helix, 19% strand | Q9Y4K3 |
| B | Ubiquitin-conjugating enzyme E2 N (EC 6.3.2.19) | protein | 148 | 33% helix, 18% strand | P61088 |
Ligands and binding sites
- ZN · Zinc ion · metal · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 103 | 0.46 | 0.79 | 16 | empty |
| 2 | 51 | 0.26 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 585 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 3HCT · Crystal structure of TRAF6 in complex with Ubc13 in the P1 space group · the same entry in another collection · chain A against A, TM-score 1.00
- 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 0.96
- Q9Y4K3 · AlphaFold monomer V2.0 prediction for TNF receptor-associated factor 6 (Q9Y4K3) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 3HCT · PDBe 3HCT · UniProt Q9Y4K3 · UniProt P61088
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