MolNFT v1 · #17121 · protein
Ternary complex of 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase
1OJ4: “Ternary complex of 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase”. X-ray diffraction, 3 ligands (CDM, ANP, CL), 2 pockets (best druggability 0.71). MolNFT v1 #17121 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1OJ4
- Type
- protein
- Length
- 566 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase
- EC
- 2.7.1.148
- UniProt
- Q8FI04
- Ligands
- CDM, ANP, CL
- Pockets
- 2 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase (EC 2.7.1.148) | protein | 283 | 34% helix, 29% strand | Q8FI04 |
Ligands and binding sites
- CDM · 4-diphosphocytidyl-2-C-methyl-D-erythritol · ligand · 2 copies · chains A, B
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 622 | 0.71 | 0.79 | 67 | CDM, ANP |
| 2 | 473 | 0.68 | 0.79 | 56 | CDM, ANP |
Interfaces
1 interface between chains.
- A–B · 538 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 1OJ4 · Ternary complex of 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase · the same entry in another collection · chain A against A, TM-score 1.00
- Q8FI04 · AlphaFold monomer V2.0 prediction for 4-diphosphocytidyl-2-C-methyl- D-erythritol kinase… · 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 Q8FI04
- Elsewhere: RCSB PDB 1OJ4 · PDBe 1OJ4 · UniProt Q8FI04
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