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Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (ispf) burkholderia pseudomallei in complex with ligand sr-4
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
- 6NMO
- Type
- protein
- Length
- 478 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
- QMS, ZN
- Pockets
- 4 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (EC 4.6.1.12) | protein | 159 | 35% helix, 31% strand | Q3JRA0 |
| C | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (EC 4.6.1.12) | protein | 160 | 33% helix, 31% strand | Q3JRA0 |
Ligands and binding sites
- QMS · N-(quinolin-8-yl)methanesulfonamide · ligand · chains A, C
- ZN · Zinc ion · metal · 3 copies · chains A, B, C
- MLI · Malonate ion · additive · 3 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · 3 copies · chains B, C
- DMS · Dimethyl sulfoxide · additive · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 271 | 0.82 | 0.94 | 46 | MLI |
| 2 | 312 | 0.67 | 0.82 | 39 | ZN, MLI, EDO |
| 3 | 307 | 0.57 | 0.77 | 34 | EDO |
| 4 | 263 | 0.56 | 0.77 | 34 | DMS, ZN, QMS |
Interfaces
3 interfaces between chains.
- B–C · 1147 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1113 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 1097 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 6NMO · 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 6NMO · PDBe 6NMO · UniProt Q3JRA0
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