Research workbench
The role of lysine 166 in the mechanism of mandelate racemase from pseudomonas putida: mechanistic and crystallographic evidence for stereospecific alkylation by (R)-alpha-phenylglycidate
Analyse The role of lysine 166 in the mechanism of mandelate racemase from pseudomonas… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1MDR
- Type
- protein
- Length
- 357 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mandelate racemase
- EC
- 5.1.2.2
- UniProt
- P11444
- Ligands
- APG, MG
- Pockets
- 2 · best druggability 0.58
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mandelate racemase (EC 5.1.2.2) | protein | 357 | 41% helix, 24% strand | P11444 |
Ligands and binding sites
- APG · Atrolactic acid (2-phenyl-lactic acid) · ligand · chains A
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 169 | 0.58 | 0.82 | 29 | APG |
| 2 | 160 | 0.49 | 0.78 | 22 | empty |
Compared structures
- 1MDR · The role of lysine 166 in the mechanism of mandelate racemase from pseudomonas putida… · the same entry in another collection · chain A against A, TM-score 1.00
- P11444 · AlphaFold monomer V2.0 prediction for mandelate racemase (P11444) · 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 P11444
- Elsewhere: RCSB PDB 1MDR · PDBe 1MDR · UniProt P11444
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