MolNFT v1 · #124070 · protein
Structure of eukaryotic translation initiation factor 3 subunit D (EIF3D) cap binding domain from nasonia vitripennis, crystal form 2
5K4C: “Structure of eukaryotic translation initiation factor 3 subunit D (EIF3D) cap binding domain from nasonia…”. X-ray diffraction, 2 pockets (best druggability 0.82). MolNFT v1 #124070 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5K4C
- Type
- protein
- Length
- 366 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Eukaryotic translation initiation factor 3 subunit D
- UniProt
- K7IM66
- Pockets
- 2 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Eukaryotic translation initiation factor 3 subunit D | protein | 366 | 29% helix, 31% strand | K7IM66 |
Ligands and binding sites
- GOL · Glycerol · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 445 | 0.82 | 0.89 | 54 | empty |
| 2 | 70 | 0.35 | 0.77 | 15 | GOL |
Compared structures
- 5K4C · 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 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 5K4C · PDBe 5K4C · UniProt K7IM66
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