Research workbench
Structure of eukaryotic translation initiation factor 3 subunit D (EIF3D) cap binding domain from nasonia vitripennis, crystal form 1
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
- 5K4B
- Type
- protein
- Length
- 722 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
- Ligands
- CL
- Pockets
- 10 · best druggability 0.88
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 | 361 | 31% helix, 31% strand | K7IM66 |
| B | Eukaryotic translation initiation factor 3 subunit D | protein | 361 | 30% helix, 31% strand | K7IM66 |
Ligands and binding sites
- CL · Chloride ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1023 | 0.88 | 0.89 | 88 | CL |
| 2 | 363 | 0.82 | 0.91 | 50 | empty |
| 3 | 301 | 0.73 | 0.86 | 40 | empty |
| 4 | 241 | 0.61 | 0.81 | 29 | empty |
| 5 | 69 | 0.52 | 0.86 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 1845 Ų buried · 39 hydrogen bonds · protein-protein
Compared structures
- 5K4B · 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 A against A, TM-score 0.99
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 5K4B · PDBe 5K4B · UniProt K7IM66
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