Research workbench
Crystal structure of ispd from mycobacterium tuberculosis in complex with CTP and mg
Analyse Crystal structure of ispd from mycobacterium tuberculosis in complex with CTP… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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
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