MolNFT v1 · #106702 · protein
Translation initiation factor EIF5B (517-858) from C. thermophilum, bound to gtpgammas and potassium
4TMZ: “Translation initiation factor EIF5B (517-858) from C. thermophilum, bound to gtpgammas and potassium”. X-ray diffraction, 4 ligands (GSP, MG, K), 11 pockets (best druggability 0.53). MolNFT v1 #106702 on GenesisL1: 3D structure…
- PDB
- 4TMZ
- Type
- protein
- Length
- 663 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- EIF5B
- Ligands
- GSP, MG, K, CL
- Pockets
- 11 · best druggability 0.53
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | EIF5B | protein | 332 | 31% helix, 29% strand | — |
| A | EIF5B | protein | 331 | 30% helix, 29% strand | — |
Ligands and binding sites
- GSP · 5'-guanosine-diphosphate-monothiophosphate · ligand · 2 copies · chains B, A
- MG · Magnesium ion · metal · 2 copies · chains B, A
- K · Potassium ion · metal · 2 copies · chains B, A
- CL · Chloride ion · ion · 2 copies · chains B
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 105 | 0.53 | 0.83 | 25 | GSP, MG, K |
| 2 | 108 | 0.50 | 0.81 | 23 | GSP, MG, K |
| 3 | 195 | 0.43 | 0.73 | 22 | empty |
| 4 | 77 | 0.41 | 0.79 | 18 | CL |
| 5 | 126 | 0.39 | 0.74 | 17 | empty |
Interfaces
1 interface between chains.
- B–A · 405 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 4TMZ · Translation initiation factor eIF5B (517-858) from C. thermophilum, bound to GTPgammaS… · the same entry in another collection · chain B against B, 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 4TMZ · PDBe 4TMZ
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