Research workbench
Crystal structure of the C-terminal domain of S. cerevisiae EIF5
Analyse Crystal structure of the C-terminal domain of S. cerevisiae EIF5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2FUL
- Type
- protein
- Length
- 970 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Eukaryotic translation initiation factor 5
- UniProt
- P38431
- Ligands
- SO4
- Pockets
- 9 · best druggability 0.64
Structure
x-ray diffraction · 6 distinct chains · 65% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Eukaryotic translation initiation factor 5 | protein | 161 | 66% helix, 0% strand | P38431 |
| B | Eukaryotic translation initiation factor 5 | protein | 159 | 66% helix, 0% strand | P38431 |
| C | Eukaryotic translation initiation factor 5 | protein | 162 | 67% helix, 1% strand | P38431 |
| D | Eukaryotic translation initiation factor 5 | protein | 163 | 64% helix, 0% strand | P38431 |
| E | Eukaryotic translation initiation factor 5 | protein | 164 | 62% helix, 1% strand | P38431 |
| F | Eukaryotic translation initiation factor 5 | protein | 161 | 66% helix, 0% strand | P38431 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 20 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 482 | 0.64 | 0.77 | 57 | empty |
| 2 | 391 | 0.61 | 0.77 | 42 | empty |
| 3 | 84 | 0.51 | 0.84 | 16 | SO4 |
| 4 | 95 | 0.45 | 0.80 | 22 | empty |
| 5 | 123 | 0.44 | 0.77 | 20 | empty |
Interfaces
7 interfaces between chains.
- C–E · 971 Ų buried · 12 hydrogen bonds · protein-protein
- D–F · 710 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 698 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 674 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 668 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 2FUL · Crystal Structure of the C-terminal Domain of S. cerevisiae eIF5 · the same entry in another collection · chain F against F, TM-score 1.00
- P38431 · AlphaFold monomer V2.0 prediction for eukaryotic translation initiation factor 5 (P38431) · a predicted model of the same protein · chain E against A, TM-score 0.94
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 P38431
- Elsewhere: RCSB PDB 2FUL · PDBe 2FUL · UniProt P38431
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