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Structure of 2C-methyl-D-erythritol-2,4-cyclodiphosphate synthase (bound form substrate)
Analyse Structure of 2C-methyl-D-erythritol-2,4-cyclodiphosphate synthase (bound form… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1IV4
- Type
- protein
- Length
- 900 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
- Q8RQP5
- Ligands
- C5P, MG
- Pockets
- 8 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (EC 4.6.1.12) | protein | 150 | 31% helix, 31% strand | Q8RQP5 |
Ligands and binding sites
- C5P · Cytidine-5'-monophosphate · ligand · 6 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 12 copies · chains A, C, B, D, F, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 185 | 0.76 | 0.92 | 35 | empty |
| 2 | 553 | 0.75 | 0.82 | 67 | MG, C5P |
| 3 | 908 | 0.73 | 0.77 | 86 | MG, C5P |
| 4 | 329 | 0.59 | 0.77 | 35 | MG, C5P |
| 5 | 323 | 0.59 | 0.77 | 31 | MG, C5P |
Interfaces
9 interfaces between chains.
- E–F · 998 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 996 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 996 Ų buried · 18 hydrogen bonds · protein-protein
- D–E · 995 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 990 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 1IV4 · Structure of 2C-Methyl-D-erythritol-2,4-cyclodiphosphate Synthase (bound form Substrate) · the same entry in another collection · chain C against C, TM-score 1.00
- Q8RQP5 · 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 1.00
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 Q8RQP5
- Elsewhere: RCSB PDB 1IV4 · PDBe 1IV4 · UniProt Q8RQP5
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