MolNFT v1 · #51478 · protein
Ispe in complex with ADP and cdp
2V8P · 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase: “Ispe in complex with ADP and cdp”. X-ray diffraction, 4 ligands (CDP, ADP, SO4), 3 pockets (best druggability 0.65). MolNFT v1 #51478 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2V8P
- Type
- protein
- Length
- 540 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
- O67060
- Ligands
- CDP, ADP, SO4, CL
- Pockets
- 3 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 28% 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 | 270 | 36% helix, 28% strand | O67060 |
Ligands and binding sites
- CDP · Cytidine-5'-diphosphate · ligand · 2 copies · chains A, B
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 381 | 0.65 | 0.79 | 45 | CDP, ADP |
| 2 | 461 | 0.65 | 0.78 | 53 | CL |
| 3 | 341 | 0.61 | 0.78 | 43 | CDP, ADP |
Interfaces
1 interface between chains.
- A–B · 424 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
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 O67060
- Elsewhere: RCSB PDB 2V8P · PDBe 2V8P · UniProt O67060
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