MolNFT v1 · #116445 · protein
Crystal structure of ispd from bacillus subtilis at 1.80 ångströms resolution, crystal form I
5DDT · 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase: “Crystal structure of ispd from bacillus subtilis at 1.80 ångströms resolution, crystal form I”. X-ray diffraction, 4 pockets (best druggability 0.84). MolNFT v1 #116445 on…
- PDB
- 5DDT
- Type
- protein
- Length
- 464 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
- Pockets
- 4 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (EC 2.7.7.60) | protein | 232 | 37% helix, 26% strand | Q06755 |
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1074 | 0.84 | 0.85 | 104 | empty |
| 2 | 80 | 0.56 | 0.87 | 21 | empty |
| 3 | 65 | 0.53 | 0.87 | 21 | empty |
| 4 | 56 | 0.28 | 0.74 | 10 | empty |
Interfaces
1 interface between chains.
- A–B · 2121 Ų buried · 41 hydrogen bonds · protein-protein
Compared structures
- 5DDT · Crystal structure of IspD from Bacillus subtilis at 1.80 Angstroms resolution, crystal… · 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 A against A, TM-score 0.95
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 5DDT · PDBe 5DDT · UniProt Q06755
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