Research workbench
Crystal structure of putative mandelate racemase / muconate lactonizing enzyme from vibrionales bacterium swat-3
Analyse Crystal structure of putative mandelate racemase / muconate lactonizing enzyme… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DFH
- Type
- protein
- Length
- 1,077 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mandelate racemase
- UniProt
- A5KUH4
- Ligands
- NA
- Pockets
- 13 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Mandelate racemase | protein | 359 | 43% helix, 17% strand | A5KUH4 |
Ligands and binding sites
- NA · Sodium ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 113 | 0.78 | 0.97 | 23 | empty |
| 2 | 835 | 0.70 | 0.76 | 89 | empty |
| 3 | 233 | 0.62 | 0.81 | 26 | empty |
| 4 | 239 | 0.60 | 0.80 | 24 | empty |
| 5 | 205 | 0.51 | 0.76 | 35 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1453 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 452 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 93 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3DFH · crystal structure of putative mandelate racemase / muconate lactonizing enzyme from… · the same entry in another collection · chain A against A, TM-score 1.00
- A5KUH4 · AlphaFold monomer V2.0 prediction for D-galactonate dehydratase family member… · a predicted model of the same protein · chain A against A, TM-score 0.98
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 A5KUH4
- Elsewhere: RCSB PDB 3DFH · PDBe 3DFH · UniProt A5KUH4
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