Research workbench
Crystal structure of mycobacterium tuberculosis NAD kinase-NAD complex
Analyse Crystal structure of mycobacterium tuberculosis NAD kinase-NAD complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1Y3I
- Type
- protein
- Length
- 462 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Inorganic POLYPHOSPHATE/ATP-NAD kinase
- EC
- 2.7.1.23
- UniProt
- P0A5S6
- Ligands
- NAD, SO4
- Pockets
- 2 · best druggability 0.47
Structure
x-ray diffraction · 1 distinct chain · 18% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Inorganic POLYPHOSPHATE/ATP-NAD kinase (EC 2.7.1.23) | protein | 231 | 18% helix, 44% strand | P0A5S6 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains B
- GOL · Glycerol · additive · 4 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 128 | 0.47 | 0.78 | 26 | empty |
| 2 | 109 | 0.39 | 0.76 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1512 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 1Y3I · Crystal Structure of Mycobacterium tuberculosis NAD kinase-NAD complex · 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 P0A5S6
- Elsewhere: RCSB PDB 1Y3I · PDBe 1Y3I · UniProt P0A5S6
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