MolNFT v1 · #122691 · protein
Crystal structure of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from bacillus subtitis
5IWX: “Crystal structure of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from bacillus subtitis”. X-ray diffraction, 1 ligand (MG), 8 pockets (best druggability 0.85). MolNFT v1 #122691 on GenesisL1: 3D structure, binding sites…
- PDB
- 5IWX
- Type
- protein
- Length
- 924 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
- MG
- Pockets
- 8 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, F | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (EC 4.6.1.12) | protein | 158 | 31% helix, 33% strand | Q06756 |
| B | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (EC 4.6.1.12) | protein | 150 | 34% helix, 35% strand | Q06756 |
| D | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (EC 4.6.1.12) | protein | 151 | 34% helix, 34% strand | Q06756 |
| E | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (EC 4.6.1.12) | protein | 149 | 34% helix, 35% strand | Q06756 |
Ligands and binding sites
- 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
8 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 309 | 0.85 | 0.95 | 33 | empty |
| 2 | 914 | 0.78 | 0.81 | 74 | MG |
| 3 | 828 | 0.72 | 0.77 | 73 | empty |
| 4 | 327 | 0.65 | 0.80 | 45 | empty |
| 5 | 291 | 0.64 | 0.81 | 42 | MG |
Interfaces
8 interfaces between chains.
- A–C · 998 Ų buried · 13 hydrogen bonds · protein-protein
- D–F · 988 Ų buried · 13 hydrogen bonds · protein-protein
- D–E · 982 Ų buried · 12 hydrogen bonds · protein-protein
- E–F · 976 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 944 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 5IWX · 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 B 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 5IWX · PDBe 5IWX · UniProt Q06756
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