Research workbench
Crystal structure of the ternary complex of L-alanine dehydrogenase from mycobacterium tuberculosis with NAD+ and pyruvate
Analyse Crystal structure of the ternary complex of L-alanine dehydrogenase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VHX
- Type
- protein
- Length
- 2,214 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alanine dehydrogenase
- EC
- 1.4.1.1
- UniProt
- P30234
- Ligands
- PYR, NAD, MG
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 5 distinct chains · 43% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alanine dehydrogenase (EC 1.4.1.1) | protein | 368 | 43% helix, 17% strand | P30234 |
| B | Alanine dehydrogenase (EC 1.4.1.1) | protein | 368 | 44% helix, 18% strand | P30234 |
| C | Alanine dehydrogenase (EC 1.4.1.1) | protein | 365 | 43% helix, 18% strand | P30234 |
| D | Alanine dehydrogenase (EC 1.4.1.1) | protein | 367 | 43% helix, 18% strand | P30234 |
| E, F | Alanine dehydrogenase (EC 1.4.1.1) | protein | 373 | 43% helix, 18% strand | P30234 |
Ligands and binding sites
- PYR · Pyruvic acid · ligand · 6 copies · chains A, B, C, D, E, F
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains E, F
- MG · Magnesium ion · metal · 3 copies · chains A, B, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1194 | 0.84 | 0.86 | 135 | empty |
| 2 | 369 | 0.75 | 0.85 | 65 | PYR, NAD |
| 3 | 799 | 0.74 | 0.79 | 73 | empty |
| 4 | 688 | 0.74 | 0.80 | 70 | empty |
| 5 | 537 | 0.73 | 0.81 | 73 | PYR |
Interfaces
12 interfaces between chains.
- B–D · 1916 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 1913 Ų buried · 17 hydrogen bonds · protein-protein
- E–F · 1812 Ų buried · 17 hydrogen bonds · protein-protein
- D–F · 714 Ų buried · 11 hydrogen bonds · protein-protein
- C–E · 690 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 2VHX · Crystal structure of the ternary complex of L-alanine dehydrogenase from Mycobacterium… · 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 2VHX · PDBe 2VHX · UniProt P30234
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