MolNFT v1 · #100942 · protein
Crystal structure of eukaryotic translation initiation factor EIF5B (399-852) from saccharomyces cerevisiae in complex with GDP
4NCF · Eukaryotic translation initiation factor 5B: “Crystal structure of eukaryotic translation initiation factor EIF5B (399-852) from saccharomyces cerevisiae…”. X-ray diffraction, 2 ligands (GDP, MG), 11 pockets (best druggability…
- PDB
- 4NCF
- Type
- protein
- Length
- 877 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Eukaryotic translation initiation factor 5B
- UniProt
- P39730
- Ligands
- GDP, MG
- Pockets
- 11 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Eukaryotic translation initiation factor 5B | protein | 448 | 36% helix, 27% strand | P39730 |
| B | Eukaryotic translation initiation factor 5B | protein | 429 | 37% helix, 29% strand | P39730 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 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
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 841 | 0.76 | 0.80 | 69 | empty |
| 2 | 496 | 0.67 | 0.78 | 80 | empty |
| 3 | 434 | 0.67 | 0.79 | 56 | empty |
| 4 | 265 | 0.59 | 0.78 | 37 | empty |
| 5 | 115 | 0.48 | 0.79 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 648 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4NCF · Crystal structure of eukaryotic translation initiation factor eIF5B (399-852) from… · the same entry in another collection · chain A against A, TM-score 1.00
- P39730 · AlphaFold monomer V2.0 prediction for eukaryotic translation initiation factor 5B (P39730) · a predicted model of the same protein · chain B against A, TM-score 0.83
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P39730
- Elsewhere: RCSB PDB 4NCF · PDBe 4NCF · UniProt P39730
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.