Research workbench
Crystal structure of holo L-alanine dehydrogenase from mycobacterium tuberculosis in the open and 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
- 2VHW
- Type
- protein
- Length
- 2,228 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
- NAI, MG
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Alanine dehydrogenase (EC 1.4.1.1) | protein | 371 | 43% helix, 18% strand | P30234 |
| B, D | Alanine dehydrogenase (EC 1.4.1.1) | protein | 370 | 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
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 6 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1157 | 0.84 | 0.85 | 110 | empty |
| 2 | 561 | 0.77 | 0.83 | 77 | NAI |
| 3 | 526 | 0.76 | 0.83 | 74 | NAI |
| 4 | 484 | 0.75 | 0.84 | 68 | NAI |
| 5 | 694 | 0.75 | 0.81 | 69 | empty |
Interfaces
12 interfaces between chains.
- B–D · 1927 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 1899 Ų buried · 17 hydrogen bonds · protein-protein
- E–F · 1815 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 725 Ų buried · 14 hydrogen bonds · protein-protein
- C–E · 719 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 2VHW · Crystal structure of holo L-alanine dehydrogenase from Mycobacterium tuberculosis in the… · the same entry in another collection · chain B against B, 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 2VHW · PDBe 2VHW · UniProt P30234
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