Research workbench
2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from salmonella typhimurium
Analyse 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from salmonella… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GHZ
- Type
- protein
- Length
- 465 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
- Q8ZMF7
- Ligands
- POP, MG
- Pockets
- 4 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (EC 4.6.1.12) | protein | 157 | 36% helix, 31% strand | Q8ZMF7 |
| B | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (EC 4.6.1.12) | protein | 151 | 33% helix, 34% strand | Q8ZMF7 |
Ligands and binding sites
- POP · Pyrophosphate 2- · ligand · chains A, B, C
- MG · Magnesium ion · metal · 4 copies · chains A, C, B
- GOL · Glycerol · additive · 2 copies · chains A, C
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 | 226 | 0.84 | 0.96 | 31 | POP |
| 2 | 237 | 0.64 | 0.82 | 34 | GOL, MG |
| 3 | 249 | 0.61 | 0.81 | 29 | MG |
| 4 | 195 | 0.61 | 0.82 | 29 | GOL, MG |
Interfaces
3 interfaces between chains.
- A–B · 1074 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 1043 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 1034 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 3GHZ · 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Salmonella typhimurium · the same entry in another collection · chain A against A, TM-score 1.00
- Q8ZMF7 · 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 0.98
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 Q8ZMF7
- Elsewhere: RCSB PDB 3GHZ · PDBe 3GHZ · UniProt Q8ZMF7
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