Research workbench
Crystal structure of mandelate RACEMASE/MUCONATE lactonizing protein from paracoccus denitrificans PD1222 complexed with magnesium
Analyse Crystal structure of mandelate RACEMASE/MUCONATE lactonizing protein from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DWD
- Type
- protein
- Length
- 741 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mandelate RACEMASE/MUCONATE lactonizing enzyme, C-terminal domain protein
- UniProt
- A1AYL4
- Ligands
- MG, CL
- Pockets
- 11 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mandelate RACEMASE/MUCONATE lactonizing enzyme, C-terminal domain protein | protein | 368 | 44% helix, 19% strand | A1AYL4 |
| B | Mandelate RACEMASE/MUCONATE lactonizing enzyme, C-terminal domain protein | protein | 373 | 43% helix, 20% strand | A1AYL4 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 289 | 0.79 | 0.91 | 44 | MG, CL |
| 2 | 182 | 0.64 | 0.84 | 24 | empty |
| 3 | 192 | 0.63 | 0.84 | 27 | empty |
| 4 | 339 | 0.58 | 0.77 | 34 | empty |
| 5 | 300 | 0.55 | 0.76 | 35 | empty |
Interfaces
1 interface between chains.
- A–B · 1717 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 23 modified (engineered).
Compared structures
- 4DWD · Crystal structure of mandelate racemase/muconate lactonizing protein from Paracoccus… · 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 A1AYL4
- Elsewhere: RCSB PDB 4DWD · PDBe 4DWD · UniProt A1AYL4
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