Research workbench
Crystal structure of holo L-alanine dehydrogenase from mycobacterium tuberculosis in the closed conformation
Analyse Crystal structure of holo L-alanine dehydrogenase from mycobacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VHZ
- Type
- protein
- Length
- 742 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alanine dehydrogenase
- EC
- 1.4.1.1
- UniProt
- P30234
- Ligands
- NAI
- Pockets
- 8 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Alanine dehydrogenase (EC 1.4.1.1) | protein | 371 | 43% helix, 18% strand | P30234 |
Ligands and binding sites
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 315 | 0.70 | 0.83 | 50 | NAI |
| 2 | 250 | 0.69 | 0.85 | 44 | NAI |
| 3 | 107 | 0.43 | 0.78 | 24 | empty |
| 4 | 95 | 0.40 | 0.77 | 25 | empty |
| 5 | 108 | 0.37 | 0.75 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1858 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 2VHZ · Crystal structure of holo L-alanine dehydrogenase from Mycobacterium tuberculosis in the… · 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 P30234
- Elsewhere: RCSB PDB 2VHZ · PDBe 2VHZ · UniProt P30234
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