Research workbench
Ternary complex of M. tuberculosis RV2780 with NAD and pyruvate
Analyse Ternary complex of M. tuberculosis RV2780 with NAD and pyruvate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VOJ
- Type
- protein
- Length
- 1,113 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alanine dehydrogenase
- EC
- 1.4.1.1
- UniProt
- P30234
- Ligands
- NAD, 2OP
- Pockets
- 16 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Alanine dehydrogenase (EC 1.4.1.1) | protein | 371 | 41% helix, 19% strand | P30234 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 3 copies · chains A, C, E
- 2OP · (2S)-2-hydroxypropanoic acid · ligand · 3 copies · chains A, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 264 | 0.74 | 0.88 | 42 | NAD, 2OP |
| 2 | 366 | 0.74 | 0.85 | 59 | NAD, 2OP |
| 3 | 240 | 0.72 | 0.87 | 44 | NAD, 2OP |
| 4 | 300 | 0.67 | 0.82 | 32 | empty |
| 5 | 407 | 0.65 | 0.78 | 41 | empty |
Interfaces
3 interfaces between chains.
- A–E · 411 Ų buried · 10 hydrogen bonds · protein-protein
- C–E · 389 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 369 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 2VOJ · Ternary complex of M. tuberculosis Rv2780 with NAD and pyruvate · 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 2VOJ · PDBe 2VOJ · UniProt P30234
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