MolNFT v1 · #106700 · protein
Translation initiation factor EIF5B (517-858) mutant D533N from C. thermophilum, bound to GTP and sodium
4TMX: “Translation initiation factor EIF5B (517-858) mutant D533N from C. thermophilum, bound to GTP and sodium”. X-ray diffraction, 3 ligands (GTP, NA, MG), 10 pockets (best druggability 0.78). MolNFT v1 #106700 on GenesisL1: 3D…
- PDB
- 4TMX
- Type
- protein
- Length
- 687 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- EIF5B
- Ligands
- GTP, NA, MG
- Pockets
- 10 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | EIF5B | protein | 342 | 33% helix, 28% strand | — |
| B | EIF5B | protein | 345 | 31% helix, 27% strand | — |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 14 copies · chains A, B
- ACY · Acetic acid · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 978 | 0.78 | 0.80 | 79 | EDO |
| 2 | 96 | 0.49 | 0.82 | 23 | GTP, NA, MG |
| 3 | 87 | 0.48 | 0.82 | 23 | GTP, NA, MG |
| 4 | 126 | 0.43 | 0.76 | 26 | empty |
| 5 | 74 | 0.41 | 0.79 | 11 | EDO |
Interfaces
1 interface between chains.
- A–B · 767 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 4TMX · Translation initiation factor eIF5B (517-858) mutant D533N from C. thermophilum, bound to… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 4TMX · PDBe 4TMX
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