Research workbench
Crystal structure of TRAF6 in complex with UBC13 in the P1 space group
Analyse Crystal structure of TRAF6 in complex with UBC13 in the P1 space group in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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