MolNFT v1 · #121327 · protein
Crystal structure of ispd complexed with CTP and MG2+ from bacillus subtilis at 1.90 ångströms resolution
5HS2 · 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase: “Crystal structure of ispd complexed with CTP and MG2+ from bacillus subtilis at 1.90 ångströms resolution”. X-ray diffraction, 2 ligands (CTP, MG), 3 pockets (best…
- PDB
- 5HS2
- Type
- protein
- Length
- 441 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
- Q06755
- Ligands
- CTP, MG
- Pockets
- 3 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 37% 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 | 226 | 36% helix, 27% strand | Q06755 |
| B | 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (EC 2.7.7.60) | protein | 215 | 37% helix, 28% strand | Q06755 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 718 | 0.84 | 0.88 | 58 | empty |
| 2 | 364 | 0.69 | 0.82 | 40 | CTP, MG |
| 3 | 76 | 0.34 | 0.76 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 2034 Ų buried · 40 hydrogen bonds · protein-protein
Compared structures
- 5HS2 · Crystal structure of IspD complexed with CTP and Mg2+ from Bacillus subtilis at 1.90… · the same entry in another collection · chain A against A, TM-score 1.00
- Q06755 · 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 0.98
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 Q06755
- Elsewhere: RCSB PDB 5HS2 · PDBe 5HS2 · UniProt Q06755
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