MolNFT v1 · #74580 · protein
Crystal structure of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from burkholderia pseudomallei with cytidine and FOL955, 4- (1H-imidazol)-1-YL)PHENOL
3P0Z: “Crystal structure of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from burkholderia pseudomallei…”. X-ray diffraction, 5 ligands (CTN, MSR, ZN), 4 pockets (best druggability 0.82). MolNFT v1 #74580 on GenesisL1: 3D…
- PDB
- 3P0Z
- Type
- protein
- Length
- 462 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
- EC
- 4.6.1.12
- UniProt
- Q3JRA0
- Ligands
- CTN, MSR, ZN, K, CL
- Pockets
- 4 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 35% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (EC 4.6.1.12) | protein | 158 | 35% helix, 30% strand | Q3JRA0 |
| B | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (EC 4.6.1.12) | protein | 151 | 35% helix, 33% strand | Q3JRA0 |
| C | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (EC 4.6.1.12) | protein | 153 | 35% helix, 33% strand | Q3JRA0 |
Ligands and binding sites
- CTN · 4-amino-1-beta-D-ribofuranosyl-2(1H)-pyrimidinone · ligand · 3 copies · chains A, C, B
- MSR · 4-(1H-imidazol-1-yl)phenol · ligand · chains A, B
- ZN · Zinc ion · metal · 3 copies · chains A, B, C
- K · Potassium ion · metal · chains A, B, C
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 245 | 0.82 | 0.94 | 48 | K |
| 2 | 314 | 0.58 | 0.77 | 37 | MSR, CTN |
| 3 | 167 | 0.45 | 0.75 | 30 | CTN |
| 4 | 159 | 0.42 | 0.74 | 29 | CTN |
Interfaces
3 interfaces between chains.
- B–C · 1165 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1119 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 1086 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 3P0Z · Crystal structure of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from… · the same entry in another collection · chain B against B, TM-score 1.00
- Q3JRA0 · AlphaFold monomer V2.0 prediction for 2-C-methyl-D-erythritol 2,4-cyclodiphosphate… · 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 Q3JRA0
- Elsewhere: RCSB PDB 3P0Z · PDBe 3P0Z · UniProt Q3JRA0
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