MolNFT v1 · #122068 · protein
TRIM5 B-BOX2 and coiled-coil chimera
5IEA · Tripartite motif-containing protein 5, serine--tRNA ligase…: “TRIM5 B-BOX2 and coiled-coil chimera”. X-ray diffraction, 1 ligand (ZN), 7 pockets (best druggability 0.63). MolNFT v1 #122068 on GenesisL1: 3D structure, binding sites…
- PDB
- 5IEA
- Type
- protein
- Length
- 708 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tripartite motif-containing protein 5, serine--tRNA ligase chimera
- EC
- 6.3.2.-, 6.1.1.11
- UniProt
- Q0PF16, P34945
- Ligands
- ZN
- Pockets
- 7 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 66% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, F, K | Tripartite motif-containing protein 5, serine--tRNA ligase chimera (EC 6.3.2.-, 6.1.1.11) | protein | 118 | 66% helix, 9% strand | Q0PF16, P34945 |
Ligands and binding sites
- ZN · Zinc ion · metal · 12 copies · chains A, B, C, D, F, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 272 | 0.63 | 0.81 | 42 | empty |
| 2 | 175 | 0.60 | 0.82 | 23 | empty |
| 3 | 321 | 0.58 | 0.76 | 35 | empty |
| 4 | 288 | 0.50 | 0.73 | 30 | empty |
| 5 | 188 | 0.44 | 0.73 | 24 | empty |
Interfaces
12 interfaces between chains.
- B–D · 336 Ų buried · 6 hydrogen bonds · protein-protein
- C–K · 336 Ų buried · 8 hydrogen bonds · protein-protein
- F–K · 335 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 334 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 334 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5IEA · TRIM5 B-box2 and coiled-coil chimera · the same entry in another collection · chain K against K, TM-score 1.00
- Q0PF16 · AlphaFold monomer V2.0 prediction for tripartite motif-containing protein 5 (Q0PF16) · a predicted model of the same protein · chain A against A, TM-score 0.59
- P34945 · AlphaFold monomer V2.0 prediction for serine--tRNA ligase (P34945) · a predicted model of the same protein · chain A against A, TM-score 0.50
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 5IEA · PDBe 5IEA · UniProt Q0PF16 · UniProt P34945
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