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Structure of mtb 2-C-methyl-D-erythritol 4-phosphate cytidyltransferase (ispd) complexed with CTP
Analyse Structure of mtb 2-C-methyl-D-erythritol 4-phosphate cytidyltransferase (ispd)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3Q7U
- 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 cytidyltransferase
- EC
- 2.7.7.60
- UniProt
- P96864
- Ligands
- CTP, MG
- Pockets
- 3 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2-C-methyl-D-erythritol 4-phosphate cytidyltransferase (EC 2.7.7.60) | protein | 222 | 38% helix, 23% strand | P96864 |
| B | 2-C-methyl-D-erythritol 4-phosphate cytidyltransferase (EC 2.7.7.60) | protein | 226 | 37% 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 835 | 0.80 | 0.83 | 69 | CTP, MG |
| 2 | 260 | 0.62 | 0.81 | 36 | MG, CTP |
| 3 | 63 | 0.33 | 0.76 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1699 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 3Q7U · Structure of Mtb 2-C-methyl-D-erythritol 4-phosphate cytidyltransferase (IspD) complexed… · 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 3Q7U · PDBe 3Q7U · UniProt P96864
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