Research workbench
Ispe in complex with ADP and cdpme
Analyse Ispe in complex with ADP and cdpme in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2V2Z
- Type
- protein
- Length
- 539 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 4-diphosphocytidyl-2C-methyl-D-erythritol kinase
- EC
- 2.7.1.148
- UniProt
- O67060
- Ligands
- CDM, ADP, SO4, CL
- Pockets
- 4 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 4-diphosphocytidyl-2C-methyl-D-erythritol kinase (EC 2.7.1.148) | protein | 269 | 38% helix, 28% strand | O67060 |
| B | 4-diphosphocytidyl-2C-methyl-D-erythritol kinase (EC 2.7.1.148) | protein | 270 | 37% helix, 28% strand | O67060 |
Ligands and binding sites
- CDM · 4-diphosphocytidyl-2-C-methyl-D-erythritol · ligand · 2 copies · chains A, B
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
- CL · Chloride ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 456 | 0.66 | 0.78 | 52 | CL |
| 2 | 387 | 0.64 | 0.79 | 46 | CDM, ADP |
| 3 | 348 | 0.64 | 0.79 | 43 | CDM, ADP |
| 4 | 64 | 0.31 | 0.75 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 434 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
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 O67060
- Elsewhere: RCSB PDB 2V2Z · PDBe 2V2Z · UniProt O67060
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