MolNFT v1 · #122692 · protein
Crystal structure of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from bacillus subtitis complexed with cmp and MG2+
5IWY: “Crystal structure of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from bacillus subtitis complexed…”. X-ray diffraction, 2 ligands (C5P, MG), 10 pockets (best druggability 0.85). MolNFT v1 #122692 on GenesisL1: 3D…
- PDB
- 5IWY
- Type
- protein
- Length
- 932 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
- Q06756
- Ligands
- C5P, MG
- Pockets
- 10 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, F | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (EC 4.6.1.12) | protein | 158 | 33% helix, 33% strand | Q06756 |
| D, E | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (EC 4.6.1.12) | protein | 150 | 35% helix, 32% strand | Q06756 |
Ligands and binding sites
- C5P · Cytidine-5'-monophosphate · ligand · 4 copies · chains A, C, B, E, F
- MG · Magnesium ion · metal · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 302 | 0.85 | 0.95 | 35 | empty |
| 2 | 267 | 0.85 | 0.95 | 33 | empty |
| 3 | 581 | 0.68 | 0.78 | 51 | empty |
| 4 | 297 | 0.66 | 0.82 | 39 | C5P |
| 5 | 331 | 0.65 | 0.81 | 42 | MG, C5P |
Interfaces
8 interfaces between chains.
- B–C · 1079 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1051 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 1029 Ų buried · 17 hydrogen bonds · protein-protein
- D–F · 1013 Ų buried · 16 hydrogen bonds · protein-protein
- E–F · 1010 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 5IWY · Crystal structure of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Bacillus… · the same entry in another collection · chain F against F, TM-score 1.00
- Q06756 · 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 Q06756
- Elsewhere: RCSB PDB 5IWY · PDBe 5IWY · UniProt Q06756
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