Research workbench
Crystal structure of ispd from mycobacterium smegmatis in complex with cmp
Analyse Crystal structure of ispd from mycobacterium smegmatis in complex with cmp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2XWM
- Type
- protein
- Length
- 442 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
- A0R560
- Ligands
- C5P
- Pockets
- 2 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (EC 2.7.7.60) | protein | 220 | 38% helix, 24% strand | A0R560 |
| B | 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (EC 2.7.7.60) | protein | 222 | 39% helix, 23% strand | A0R560 |
Ligands and binding sites
- C5P · Cytidine-5'-monophosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1096 | 0.82 | 0.83 | 96 | C5P |
| 2 | 59 | 0.28 | 0.74 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 1595 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 2XWM · Crystal structure of IspD from Mycobacterium smegmatis in complex with CMP · 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 A0R560
- Elsewhere: RCSB PDB 2XWM · PDBe 2XWM · UniProt A0R560
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