Research workbench
Crystal structure of 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (ispd) in complex with 1,2-propanediol
Analyse Crystal structure of 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3N9W
- Type
- protein
- Length
- 415 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
- EC
- 2.7.7.60
- UniProt
- Q46893
- Pockets
- 4 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (EC 2.7.7.60) | protein | 195 | 35% helix, 27% strand | Q46893 |
| B | 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (EC 2.7.7.60) | protein | 220 | 32% helix, 26% strand | Q46893 |
Ligands and binding sites
- PGO · S-1,2-propanediol · additive · 2 copies · chains A, B
- PGR · R-1,2-propanediol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 329 | 0.71 | 0.84 | 34 | PGO |
| 2 | 163 | 0.48 | 0.77 | 31 | PGR |
| 3 | 89 | 0.37 | 0.76 | 18 | empty |
| 4 | 51 | 0.31 | 0.77 | 14 | PGO |
Interfaces
1 interface between chains.
- A–B · 2107 Ų buried · 45 hydrogen bonds · protein-protein
Compared structures
- 3N9W · Crystal structure of 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (IspD) in… · the same entry in another collection · chain B against B, TM-score 1.00
- Q46893 · AlphaFold monomer V2.0 prediction for 2-C-methyl-D-erythritol 4-phosphate… · a predicted model of the same protein · chain B against A, TM-score 0.97
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 Q46893
- Elsewhere: RCSB PDB 3N9W · PDBe 3N9W · UniProt Q46893
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