MolNFT v1 · #53488 · protein
A triclinic crystal form of E. COLI 4-diphosphocytidyl-2C- methyl-D-erythritol kinase
2WW4 · 4-diphosphocytidyl-2C-methyl-D-erythritol kinase: “A triclinic crystal form of E. COLI 4-diphosphocytidyl-2C- methyl-D-erythritol kinase”. X-ray diffraction, 1 ligand (ADP), 5 pockets (best druggability 0.83). MolNFT v1 #53488 on…
- PDB
- 2WW4
- Type
- protein
- Length
- 565 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 4-diphosphocytidyl-2C-methyl-D-erythritol kinase
- EC
- 2.7.1.148
- UniProt
- B7LXC3
- Ligands
- ADP
- Pockets
- 5 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 4-diphosphocytidyl-2C-methyl-D-erythritol kinase (EC 2.7.1.148) | protein | 283 | 33% helix, 29% strand | B7LXC3 |
| B | 4-diphosphocytidyl-2C-methyl-D-erythritol kinase (EC 2.7.1.148) | protein | 282 | 33% helix, 29% strand | B7LXC3 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 863 | 0.83 | 0.86 | 114 | ADP |
| 2 | 240 | 0.62 | 0.81 | 30 | empty |
| 3 | 199 | 0.55 | 0.79 | 24 | empty |
| 4 | 194 | 0.52 | 0.77 | 23 | empty |
| 5 | 91 | 0.39 | 0.77 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1113 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 2WW4 · a triclinic crystal form of E. coli 4-diphosphocytidyl-2C-methyl-D- erythritol kinase · the same entry in another collection · chain A against A, TM-score 1.00
- B7LXC3 · AlphaFold monomer V2.0 prediction for 4-diphosphocytidyl-2-C-methyl- D-erythritol kinase… · a predicted model of the same protein · chain B against A, TM-score 0.98
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 B7LXC3
- Elsewhere: RCSB PDB 2WW4 · PDBe 2WW4 · UniProt B7LXC3
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