Research workbench
The 1.9 a crystal structure of alanine racemase from mycobacterium tuberculosis contains a conserved entryway into the active site
Analyse The 1.9 a crystal structure of alanine racemase from mycobacterium tuberculosis… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1XFC
- Type
- protein
- Length
- 722 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alanine racemase
- EC
- 5.1.1.1
- UniProt
- P0A4X2
- Ligands
- PLP
- Pockets
- 8 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alanine racemase (EC 5.1.1.1) | protein | 366 | 35% helix, 25% strand | P0A4X2 |
| B | Alanine racemase (EC 5.1.1.1) | protein | 356 | 35% helix, 24% strand | P0A4X2 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 182 | 0.78 | 0.93 | 39 | PLP |
| 2 | 555 | 0.71 | 0.80 | 54 | PLP |
| 3 | 228 | 0.54 | 0.77 | 42 | empty |
| 4 | 206 | 0.54 | 0.78 | 45 | empty |
| 5 | 118 | 0.49 | 0.80 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 2020 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 1XFC · The 1.9 A crystal structure of alanine racemase from Mycobacterium tuberculosis contains… · 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 P0A4X2
- Elsewhere: RCSB PDB 1XFC · PDBe 1XFC · UniProt P0A4X2
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