Research workbench
Translation initiation factor EIF5B (517-858) from C. thermophilum, bound to GTP and sodium
Analyse Translation initiation factor EIF5B (517-858) from C. thermophilum, bound to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4TMW
- Type
- protein
- Length
- 688 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- EIF5B
- Ligands
- GTP, NA, MG
- Pockets
- 8 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | EIF5B | protein | 343 | 33% helix, 29% strand | — |
| B | EIF5B | protein | 345 | 33% helix, 29% 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
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1120 | 0.77 | 0.79 | 74 | empty |
| 2 | 163 | 0.53 | 0.80 | 24 | empty |
| 3 | 98 | 0.51 | 0.83 | 24 | GTP, NA, MG |
| 4 | 93 | 0.48 | 0.82 | 23 | GTP, NA, MG |
| 5 | 101 | 0.36 | 0.74 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 743 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4TMW · Translation initiation factor eIF5B (517-858) from C. thermophilum, bound to GTP and… · 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 4TMW · PDBe 4TMW
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