MolNFT v1 · #138131 · protein
The structure of the TRIM5ALPHA bbox- coiled coil in complex LC3B
5W9A · Tripartite motif-containing protein 5: “The structure of the TRIM5ALPHA bbox- coiled coil in complex LC3B”. X-ray diffraction, 1 ligand (ZN), 6 pockets (best druggability 0.75). MolNFT v1 #138131 on GenesisL1: 3D structure, binding…
- PDB
- 5W9A
- Type
- protein
- Length
- 611 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tripartite motif-containing protein 5; Microtubule-associated proteins 1A/1B light chain…
- EC
- 2.3.2.27
- UniProt
- Q0PF16, Q9GZQ8
- Ligands
- ZN
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 56% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tripartite motif-containing protein 5 (EC 2.3.2.27) | protein | 193 | 71% helix, 4% strand | Q0PF16 |
| C | Microtubule-associated proteins 1A/1B light chain 3B | protein | 114 | 32% helix, 23% strand | Q9GZQ8 |
| D | Microtubule-associated proteins 1A/1B light chain 3B | protein | 113 | 33% helix, 23% strand | Q9GZQ8 |
| B | Tripartite motif-containing protein 5 (EC 2.3.2.27) | protein | 191 | 70% helix, 5% strand | Q0PF16 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 404 | 0.75 | 0.85 | 49 | empty |
| 2 | 53 | 0.36 | 0.80 | 15 | empty |
| 3 | 89 | 0.34 | 0.74 | 22 | empty |
| 4 | 74 | 0.34 | 0.76 | 18 | empty |
| 5 | 52 | 0.28 | 0.75 | 10 | empty |
Interfaces
5 interfaces between chains.
- A–B · 4819 Ų buried · 28 hydrogen bonds · protein-protein
- A–C · 886 Ų buried · 11 hydrogen bonds · protein-protein
- D–B · 879 Ų buried · 17 hydrogen bonds · protein-protein
- C–B · 140 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 114 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5W9A · The structure of the Trim5alpha Bbox- coiled coil in complex LC3B · the same entry in another collection · chain B against B, TM-score 1.00
- Q9GZQ8 · AlphaFold monomer V2.0 prediction for microtubule-associated proteins 1A/1B light chain… · a predicted model of the same protein · chain D against A, TM-score 0.96
- 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 0.81
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 Q0PF16
- Every structure of UniProt Q9GZQ8
- Elsewhere: RCSB PDB 5W9A · PDBe 5W9A · UniProt Q0PF16 · UniProt Q9GZQ8
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