MolNFT v1 · #157361 · protein
Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (ispf) burkholderia pseudomallei in complex with ligand hgn- 0459
6MWF · 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase: “Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (ispf) burkholderia pseudomallei in…”. X-ray diffraction, 2 ligands (SFY, ZN), 4 pockets (best…
- PDB
- 6MWF
- Type
- protein
- Length
- 474 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
- SFY, ZN
- Pockets
- 4 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 32% 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, 32% strand | Q3JRA0 |
| C | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (EC 4.6.1.12) | protein | 156 | 34% helix, 33% strand | Q3JRA0 |
Ligands and binding sites
- SFY · 4-amino-N-(pyridin-2-yl)benzenesulfonamide · ligand · 2 copies · chains A, B, C
- ZN · Zinc ion · metal · 3 copies · chains A, B, C
- DMS · Dimethyl sulfoxide · additive · chains A
- ACT · Acetate ion · 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 | 0.83 | 0.94 | 47 | empty |
| 2 | 275 | 0.61 | 0.79 | 38 | SFY |
| 3 | 287 | 0.56 | 0.77 | 36 | empty |
| 4 | 277 | 0.55 | 0.76 | 42 | DMS, ZN, SFY |
Interfaces
3 interfaces between chains.
- B–C · 1127 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 1089 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 1065 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 6MWF · 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 6MWF · PDBe 6MWF · UniProt Q3JRA0
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.