Research workbench
Structure of mtb 2-C-methyl-D-erythritol 4-phosphate cytidyltransferase (ispd) complexed with cdp-me
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
- 3Q80
- Type
- protein
- Length
- 436 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
- CDM, MG, CL
- Pockets
- 3 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 39% 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 | 218 | 40% helix, 23% strand | P96864 |
| B | 2-C-methyl-D-erythritol 4-phosphate cytidyltransferase (EC 2.7.7.60) | protein | 218 | 38% helix, 23% strand | P96864 |
Ligands and binding sites
- CDM · 4-diphosphocytidyl-2-C-methyl-D-erythritol · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains B
- CL · Chloride ion · ion · 4 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 | 486 | 0.85 | 0.91 | 38 | empty |
| 2 | 323 | 0.66 | 0.82 | 37 | CDM, MG, CL |
| 3 | 294 | 0.64 | 0.81 | 35 | CDM, MG, CL |
Interfaces
1 interface between chains.
- A–B · 1905 Ų buried · 35 hydrogen bonds · protein-protein
Compared structures
- 3Q80 · 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 3Q80 · PDBe 3Q80 · UniProt P96864
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