Research workbench
Translation initiation factor EIF5B (517-858) mutant D533A from C. thermophilum, bound to gtpgammas
Analyse Translation initiation factor EIF5B (517-858) mutant D533A from C.… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4TMT
- Type
- protein
- Length
- 687 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- EIF5B
- Ligands
- GSP, MG, CL
- Pockets
- 8 · best druggability 0.77
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, 29% strand | — |
| B | EIF5B | protein | 345 | 31% helix, 28% strand | — |
Ligands and binding sites
- GSP · 5'-guanosine-diphosphate-monothiophosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 12 copies · chains A, B
- DTT · 2,3-dihydroxy-1,4-dithiobutane · additive · chains A
- ACY · Acetic acid · additive · chains 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1080 | 0.77 | 0.79 | 72 | EDO, CL |
| 2 | 135 | 0.52 | 0.81 | 28 | GSP, MG |
| 3 | 99 | 0.46 | 0.80 | 24 | GSP, MG |
| 4 | 95 | 0.39 | 0.76 | 14 | EDO, CL |
| 5 | 109 | 0.39 | 0.75 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 765 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 4TMT · Translation initiation factor eIF5B (517-858) mutant D533A 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 4TMT · PDBe 4TMT
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