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Crystal structure of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from salmonella typhimurium bound to cytidine
Analyse Crystal structure of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3T80
- Type
- protein
- Length
- 915 residues
- Chains
- 6
- 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
- CTN, POP, MG, ZN
- Pockets
- 11 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 35% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, E | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (EC 4.6.1.12) | protein | 157 | 36% helix, 30% strand | Q8ZMF7 |
| B | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (EC 4.6.1.12) | protein | 147 | 35% helix, 35% strand | Q8ZMF7 |
| C | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (EC 4.6.1.12) | protein | 151 | 35% helix, 34% strand | Q8ZMF7 |
| F | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (EC 4.6.1.12) | protein | 146 | 33% helix, 36% strand | Q8ZMF7 |
Ligands and binding sites
- CTN · 4-amino-1-beta-D-ribofuranosyl-2(1H)-pyrimidinone · ligand · 6 copies · chains A, B, C, D, E, F
- POP · Pyrophosphate 2- · ligand · 2 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 8 copies · chains A, C, B, D, F, E
- ZN · Zinc ion · metal · 6 copies · chains A, B, C, D, E, F
- EDO · 1,2-ethanediol · additive · 14 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 272 | 0.85 | 0.96 | 33 | POP, EDO |
| 2 | 256 | 0.85 | 0.96 | 32 | EDO, POP |
| 3 | 289 | 0.65 | 0.81 | 33 | MG, CTN |
| 4 | 308 | 0.62 | 0.79 | 30 | ZN, MG, CTN, EDO |
| 5 | 263 | 0.59 | 0.79 | 32 | CTN, ZN, MG |
Interfaces
7 interfaces between chains.
- D–E · 1043 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 1029 Ų buried · 16 hydrogen bonds · protein-protein
- D–F · 1028 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 1022 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1005 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 3T80 · Crystal structure of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from… · the same entry in another collection · chain F against F, 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 C 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 Q8ZMF7
- Elsewhere: RCSB PDB 3T80 · PDBe 3T80 · UniProt Q8ZMF7
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