Research workbench
Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
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
- 1VHA
- Type
- protein
- Length
- 914 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
- P44815
- Ligands
- POP, MN
- Pockets
- 16 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 35% 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 | 153 | 33% helix, 35% strand | P44815 |
| B, D, E, F | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (EC 4.6.1.12) | protein | 152 | 34% helix, 36% strand | P44815 |
Ligands and binding sites
- POP · Pyrophosphate 2- · ligand · 2 copies · chains A, B, C, D, E, F
- MN · Manganese (II) ion · metal · 5 copies · chains A, B, C, D, E, F
- ACY · Acetic acid · additive · 6 copies · chains A, C, B, D, F, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 257 | 0.85 | 0.97 | 31 | ACY, POP |
| 2 | 251 | 0.85 | 0.97 | 33 | POP, ACY |
| 3 | 400 | 0.61 | 0.76 | 31 | empty |
| 4 | 282 | 0.57 | 0.78 | 30 | MN |
| 5 | 224 | 0.56 | 0.78 | 26 | MN |
Interfaces
7 interfaces between chains.
- D–E · 1205 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 1165 Ų buried · 18 hydrogen bonds · protein-protein
- D–F · 1160 Ų buried · 20 hydrogen bonds · protein-protein
- E–F · 1137 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1128 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 1VHA · Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase · the same entry in another collection · chain F against F, TM-score 1.00
- P44815 · AlphaFold monomer V2.0 prediction for 2-C-methyl-D-erythritol 2,4-cyclodiphosphate… · a predicted model of the same protein · chain B against A, TM-score 0.85
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 P44815
- Elsewhere: RCSB PDB 1VHA · PDBe 1VHA · UniProt P44815
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