MolNFT v1 · #81648 · protein
P. putida mandelate racemase co-crystallized with the intermediate analogue cupferron
3UXL: “P. putida mandelate racemase co-crystallized with the intermediate analogue cupferron”. X-ray diffraction, 2 ligands (CFI, MG), 16 pockets (best druggability 0.82). MolNFT v1 #81648 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3UXL
- 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
- CFI, MG
- Pockets
- 16 · 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
- CFI · 1-hydroxy-2-oxo-1-phenylhydrazine · 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
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1033 | 0.82 | 0.83 | 84 | empty |
| 2 | 62 | 0.73 | 0.98 | 17 | CFI |
| 3 | 57 | 0.73 | 0.98 | 15 | CFI |
| 4 | 61 | 0.73 | 0.98 | 16 | CFI |
| 5 | 599 | 0.72 | 0.80 | 80 | empty |
Interfaces
6 interfaces between chains.
- B–D · 1561 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 1560 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 492 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 101 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 59 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3UXL · P. putida mandelate racemase co-crystallized with the intermediate analogue cupferron · 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 3UXL · PDBe 3UXL · UniProt P11444
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