Research workbench
Complex of UBC13 with the ring domain of the TRIM5ALPHA retroviral restriction factor
Analyse Complex of UBC13 with the ring domain of the TRIM5ALPHA retroviral restriction… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4TKP
- Type
- protein
- Length
- 208 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin-conjugating enzyme E2 N; Tripartite motif-containing protein 5
- EC
- 6.3.2.19, 6.3.2.-
- UniProt
- P61088, Q0PF16
- Ligands
- ZN, SO4
- Pockets
- 2 · best druggability 0.38
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin-conjugating enzyme E2 N (EC 6.3.2.19) | protein | 145 | 35% helix, 18% strand | P61088 |
| B | Tripartite motif-containing protein 5 (EC 6.3.2.-) | protein | 63 | 29% helix, 16% strand | Q0PF16 |
Ligands and binding sites
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 | 72 | 0.38 | 0.78 | 14 | empty |
| 2 | 71 | 0.32 | 0.74 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 445 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4TKP · Complex of Ubc13 with the RING domain of the TRIM5alpha retroviral restriction factor · the same entry in another collection · chain B against B, 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 A against A, TM-score 0.98
- Q0PF16 · AlphaFold monomer V2.0 prediction for tripartite motif-containing protein 5 (Q0PF16) · a predicted model of the same protein · chain B 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 P61088
- Every structure of UniProt Q0PF16
- Elsewhere: RCSB PDB 4TKP · PDBe 4TKP · UniProt P61088 · UniProt Q0PF16
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