Research workbench
Crystal structure of a translation initiation complex
Analyse Crystal structure of a translation initiation complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VSX
- Type
- protein
- Length
- 1,209 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent RNA helicase EIF4A; Eukaryotic initiation factor 4F subunit P150
- EC
- 3.6.1.-
- UniProt
- P10081, P39935
- Ligands
- AMP
- Pockets
- 17 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 56% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | ATP-dependent RNA helicase EIF4A (EC 3.6.1.-) | protein | 366 | 39% helix, 19% strand | P10081 |
| E | Eukaryotic initiation factor 4F subunit P150 | protein | 240 | 69% helix, 1% strand | P39935 |
| F | Eukaryotic initiation factor 4F subunit P150 | protein | 237 | 70% helix, 1% strand | P39935 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 114 | 0.73 | 0.94 | 28 | empty |
| 2 | 116 | 0.71 | 0.93 | 26 | empty |
| 3 | 75 | 0.60 | 0.89 | 25 | empty |
| 4 | 339 | 0.60 | 0.77 | 43 | empty |
| 5 | 357 | 0.59 | 0.76 | 40 | empty |
Interfaces
5 interfaces between chains.
- A–E · 1471 Ų buried · 34 hydrogen bonds · protein-protein
- B–F · 1425 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 1183 Ų buried · 18 hydrogen bonds · protein-protein
- B–E · 134 Ų buried · 0 hydrogen bonds · protein-protein
- A–F · 128 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2VSX · Crystal Structure of a Translation Initiation Complex · the same entry in another collection · chain A against A, TM-score 1.00
- P39935 · AlphaFold monomer V2.0 prediction for eukaryotic initiation factor 4F subunit P150… · a predicted model of the same protein · chain E against A, TM-score 0.99
- P10081 · AlphaFold monomer V2.0 prediction for ATP-dependent RNA helicase EIF4A (P10081) · a predicted model of the same protein · chain A against A, TM-score 0.63
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 P10081
- Every structure of UniProt P39935
- Elsewhere: RCSB PDB 2VSX · PDBe 2VSX · UniProt P10081 · UniProt P39935
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