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Structure of eukaryotic translation initiation factor 3 subunit D (EIF3D) cap binding domain from nasonia vitripennis, crystal form 3
Analyse Structure of eukaryotic translation initiation factor 3 subunit D (EIF3D) cap… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5K4D
- Type
- protein
- Length
- 705 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Eukaryotic translation initiation factor 3 subunit D
- UniProt
- K7IM66
- Pockets
- 7 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Eukaryotic translation initiation factor 3 subunit D | protein | 356 | 30% helix, 29% strand | K7IM66 |
| B | Eukaryotic translation initiation factor 3 subunit D | protein | 349 | 30% helix, 32% strand | K7IM66 |
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 445 | 0.82 | 0.90 | 54 | empty |
| 2 | 322 | 0.82 | 0.92 | 41 | empty |
| 3 | 704 | 0.77 | 0.82 | 89 | empty |
| 4 | 124 | 0.61 | 0.86 | 21 | empty |
| 5 | 94 | 0.52 | 0.83 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 800 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 5K4D · Structure of eukaryotic translation initiation factor 3 subunit D (eIF3d) cap binding… · the same entry in another collection · chain A against A, TM-score 1.00
- K7IM66 · AlphaFold monomer V2.0 prediction for eukaryotic translation initiation factor 3 subunit… · a predicted model of the same protein · chain B 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
- Every structure of UniProt K7IM66
- Elsewhere: RCSB PDB 5K4D · PDBe 5K4D · UniProt K7IM66
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