Research workbench
Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (ispf) burkholderia pseudomallei in complex with ligand hgn- 0456
Analyse Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MWI
- Type
- protein
- Length
- 477 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
- EZL, ZN
- Pockets
- 4 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 34% helix, 31% 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 | 159 | 35% helix, 31% strand | Q3JRA0 |
| B | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (EC 4.6.1.12) | protein | 160 | 33% helix, 31% strand | Q3JRA0 |
| C | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (EC 4.6.1.12) | protein | 158 | 34% helix, 32% strand | Q3JRA0 |
Ligands and binding sites
- EZL · 6-ethoxy-1,3-benzothiazole-2-sulfonamide · ligand · chains B, C
- ZN · Zinc ion · metal · 3 copies · chains A, B, C
- DMS · Dimethyl sulfoxide · additive · 2 copies · chains A, C
- ACT · Acetate ion · additive · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 272 | 0.82 | 0.94 | 47 | empty |
| 2 | 229 | 0.60 | 0.80 | 39 | PEG |
| 3 | 326 | 0.57 | 0.76 | 40 | EZL, DMS |
| 4 | 210 | 0.51 | 0.76 | 31 | DMS |
Interfaces
3 interfaces between chains.
- A–B · 1135 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 1131 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 1109 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 6MWI · Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (IspF)… · the same entry in another collection · chain A against A, 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 6MWI · PDBe 6MWI · UniProt Q3JRA0
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