Research workbench
Effect of a Y265F mutant on the transamination based cycloserine inactivation of alanine racemase
Analyse Effect of a Y265F mutant on the transamination based cycloserine inactivation… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1XQL
- Type
- protein
- Length
- 762 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alanine racemase
- EC
- 5.1.1.1
- UniProt
- P10724
- Ligands
- PMP, PMH, PLP, 4AX
- Pockets
- 9 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alanine racemase (EC 5.1.1.1) | protein | 382 | 34% helix, 27% strand | P10724 |
| B | Alanine racemase (EC 5.1.1.1) | protein | 380 | 33% helix, 27% strand | P10724 |
Ligands and binding sites
- PMP · 4'-deoxy-4'-aminopyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- PMH · (5-hydroxy-4-{[(3-hydroxyisoxazol-4-yl)amino]methyl}-6-methylpyridin-3-yl)methyl dihydrogen phosphate · ligand · 2 copies · chains A, B
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- 4AX · (R)-4-amino-isoxazolidin-3-one · ligand · 2 copies · chains A, B
- ACY · Acetic acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 281 | 0.78 | 0.90 | 52 | 4AX, ACY, PMP, PMH, PLP |
| 2 | 349 | 0.78 | 0.88 | 70 | PMP, PMH, PLP, 4AX, ACY |
| 3 | 346 | 0.72 | 0.84 | 71 | empty |
| 4 | 71 | 0.63 | 0.91 | 26 | empty |
| 5 | 98 | 0.51 | 0.82 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 3259 Ų buried · 42 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (carboxylation).
Compared structures
- 1XQL · Effect of a Y265F Mutant on the Transamination Based Cycloserine Inactivation of Alanine… · the same entry in another collection · chain A against A, TM-score 1.00
- P10724 · AlphaFold monomer V2.0 prediction for alanine racemase (P10724) · a predicted model of the same protein · 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 P10724
- Elsewhere: RCSB PDB 1XQL · PDBe 1XQL · UniProt P10724
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