MolNFT v1 · #75714 · protein
Mycobacterium tuberculosis 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase (ispe) in complex with ADP
3PYG: “Mycobacterium tuberculosis 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase (ispe) in complex with ADP”. X-ray diffraction, 1 ligand (ADP), 2 pockets (best druggability 0.64). MolNFT v1 #75714 on GenesisL1: 3D structure, binding…
- PDB
- 3PYG
- Type
- protein
- Length
- 298 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase
- EC
- 2.7.1.148
- UniProt
- P65178
- Ligands
- ADP
- Pockets
- 2 · best druggability 0.64
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase (EC 2.7.1.148) | protein | 298 | 37% helix, 28% strand | P65178 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
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 | 428 | 0.64 | 0.78 | 54 | ADP |
| 2 | 95 | 0.43 | 0.79 | 22 | empty |
Compared structures
- 3PYG · Mycobacterium tuberculosis 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase (IspE) in… · 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 P65178
- Elsewhere: RCSB PDB 3PYG · PDBe 3PYG · UniProt P65178
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