MolNFT v1 · #118627 · protein
TRIM5 B-BOX2 and coiled-coil chimera
5F7T · Tripartite motif-containing protein 5,SERINE--tRNA ligase…: “TRIM5 B-BOX2 and coiled-coil chimera”. X-ray diffraction, 1 ligand (ZN), 3 pockets (best druggability 0.63). MolNFT v1 #118627 on GenesisL1: 3D structure, binding sites…
- PDB
- 5F7T
- Type
- protein
- Length
- 532 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tripartite motif-containing protein 5,SERINE--tRNA ligase, tripartite motif-containing…
- EC
- 6.3.2.-, 6.1.1.11
- UniProt
- Q0PF16, P34945
- Ligands
- ZN
- Pockets
- 3 · best druggability 0.63
Structure
x-ray diffraction · 3 distinct chains · 71% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | Tripartite motif-containing protein 5,SERINE--tRNA ligase, tripartite motif-containing protein 5 (EC 6.3.2.-, 6.1.1.11) | protein | 134 | 72% helix, 8% strand | Q0PF16, P34945 |
| F | Tripartite motif-containing protein 5,SERINE--tRNA ligase, tripartite motif-containing protein 5 (EC 6.3.2.-, 6.1.1.11) | protein | 132 | 71% helix, 8% strand | Q0PF16, P34945 |
| H, L | Tripartite motif-containing protein 5,SERINE--tRNA ligase, tripartite motif-containing protein 5 (EC 6.3.2.-, 6.1.1.11) | protein | 133 | 71% helix, 8% strand | Q0PF16, P34945 |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains E, F, H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 508 | 0.63 | 0.75 | 28 | empty |
| 2 | 148 | 0.43 | 0.75 | 22 | empty |
| 3 | 124 | 0.41 | 0.75 | 21 | empty |
Interfaces
4 interfaces between chains.
- E–F · 756 Ų buried · 10 hydrogen bonds · protein-protein
- F–L · 492 Ų buried · 7 hydrogen bonds · protein-protein
- E–H · 476 Ų buried · 6 hydrogen bonds · protein-protein
- H–L · 302 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 5F7T · TRIM5 B-box2 and coiled-coil chimera · the same entry in another collection · chain E against E, TM-score 1.00
- P34945 · AlphaFold monomer V2.0 prediction for serine--tRNA ligase (P34945) · a predicted model of the same protein · chain H against A, TM-score 0.53
- Q0PF16 · AlphaFold monomer V2.0 prediction for tripartite motif-containing protein 5 (Q0PF16) · a predicted model of the same protein · chain H against A, TM-score 0.41
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 P34945
- Elsewhere: RCSB PDB 5F7T · PDBe 5F7T · UniProt Q0PF16 · UniProt P34945
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