Research workbench
P. putida mandelate racemase co-crystallized with the intermediate analogue benzohydroxamate
Analyse P. putida mandelate racemase co-crystallized with the intermediate analogue… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3UXK
- Type
- protein
- Length
- 1,428 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mandelate racemase
- EC
- 5.1.2.2
- UniProt
- P11444
- Ligands
- BHO, MG
- Pockets
- 17 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Mandelate racemase (EC 5.1.2.2) | protein | 357 | 39% helix, 24% strand | P11444 |
Ligands and binding sites
- BHO · Benzhydroxamic acid · ligand · 4 copies · chains A, C, B, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1091 | 0.82 | 0.83 | 74 | empty |
| 2 | 65 | 0.72 | 0.97 | 19 | BHO |
| 3 | 64 | 0.72 | 0.97 | 18 | BHO |
| 4 | 578 | 0.72 | 0.80 | 77 | empty |
| 5 | 575 | 0.71 | 0.80 | 76 | empty |
Interfaces
6 interfaces between chains.
- A–C · 1554 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 1541 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 488 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 83 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 58 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3UXK · P. putida mandelate racemase co-crystallized with the intermediate analogue… · 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 0.99
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 3UXK · PDBe 3UXK · UniProt P11444
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