MolNFT v1 · #54683 · protein
Crystal structure of ispd from mycobacterium tuberculosis in complex with CTP and mg
2XWN · 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase: “Crystal structure of ispd from mycobacterium tuberculosis in complex with CTP and mg”. X-ray diffraction, 2 ligands (CTP, MG), 3 pockets (best druggability 0.81). MolNFT v1…
- PDB
- 2XWN
- Type
- protein
- Length
- 448 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
- P96864
- Ligands
- CTP, MG
- Pockets
- 3 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (EC 2.7.7.60) | protein | 221 | 37% helix, 23% strand | P96864 |
| B | 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (EC 2.7.7.60) | protein | 227 | 34% helix, 23% strand | P96864 |
Ligands and binding sites
- CTP · Cytidine-5'-triphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 605 | 0.81 | 0.86 | 36 | empty |
| 2 | 274 | 0.68 | 0.84 | 37 | MG, CTP |
| 3 | 236 | 0.65 | 0.83 | 35 | MG, CTP |
Interfaces
1 interface between chains.
- A–B · 1795 Ų buried · 32 hydrogen bonds · protein-protein
Compared structures
- 2XWN · Crystal structure of IspD from Mycobacterium tuberculosis in complex with CTP and Mg · the same entry in another collection · chain A against A, TM-score 1.00
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 P96864
- Elsewhere: RCSB PDB 2XWN · PDBe 2XWN · UniProt P96864
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.