Research workbench
Translation initiation factor EIF5B (517-858) from C. thermophilum, bound to gtpgammas 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
- 4TMV
- Type
- protein
- Length
- 684 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- EIF5B
- Ligands
- GSP, MG, NA
- Pockets
- 10 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | EIF5B | protein | 345 | 32% helix, 28% strand | — |
| A | EIF5B | protein | 339 | 32% 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
- NA · Sodium ion · metal · 2 copies · chains B, A
- GOL · Glycerol · additive · 7 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1078 | 0.75 | 0.77 | 75 | GOL |
| 2 | 111 | 0.53 | 0.82 | 23 | GSP, MG, NA |
| 3 | 93 | 0.52 | 0.84 | 24 | GSP, MG, NA |
| 4 | 75 | 0.34 | 0.76 | 15 | empty |
| 5 | 87 | 0.32 | 0.73 | 20 | empty |
Interfaces
1 interface between chains.
- B–A · 669 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 4TMV · 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 4TMV · PDBe 4TMV
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