MolNFT v1 · #114299 · protein
X-ray crystal structure of a 2-C-methyl-D-erythritol 2,4- cyclodiphosphate synthase from pseudomonas aeruginosa
5B8F · 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase: “X-ray crystal structure of a 2-C-methyl-D-erythritol 2,4- cyclodiphosphate synthase from pseudomonas…”. X-ray diffraction, 3 ligands (C5P, MG, PO4), 4 pockets (best…
- PDB
- 5B8F
- Type
- protein
- Length
- 481 residues
- Chains
- 3
- 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
- P57708
- Ligands
- C5P, MG, PO4
- Pockets
- 4 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 35% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (EC 4.6.1.12) | protein | 159 | 35% helix, 33% strand | P57708 |
| B | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (EC 4.6.1.12) | protein | 158 | 35% helix, 33% strand | P57708 |
| C | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (EC 4.6.1.12) | protein | 164 | 34% helix, 32% strand | P57708 |
Ligands and binding sites
- C5P · Cytidine-5'-monophosphate · ligand · 3 copies · chains A, B, C
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
- PO4 · Phosphate ion · ion · 4 copies · chains A, B, C
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 206 | 0.82 | 0.96 | 32 | PO4 |
| 2 | 352 | 0.65 | 0.80 | 44 | C5P, MG |
| 3 | 302 | 0.62 | 0.80 | 33 | MG, C5P |
| 4 | 271 | 0.56 | 0.77 | 32 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1103 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1021 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 1010 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 5B8F · X-ray Crystal Structure of a 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from… · the same entry in another collection · chain A against A, TM-score 1.00
- P57708 · 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 P57708
- Elsewhere: RCSB PDB 5B8F · PDBe 5B8F · UniProt P57708
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