MolNFT v1 · #76426 · protein
Crystal structure of D-mannonate dehydratase from chromohalobacter salexigens complexed with mg and D-gluconate
3QKE · Mandelate RACEMASE/MUCONATE lactonizing enzyme: “Crystal structure of D-mannonate dehydratase from chromohalobacter salexigens complexed with mg and…”. X-ray diffraction, 2 ligands (GCO, MG), 20 pockets (best druggability 0.89).…
- PDB
- 3QKE
- Type
- protein
- Length
- 3,174 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mandelate RACEMASE/MUCONATE lactonizing enzyme
- UniProt
- Q1QT89
- Ligands
- GCO, MG
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, G, H | Mandelate RACEMASE/MUCONATE lactonizing enzyme | protein | 397 | 39% helix, 21% strand | Q1QT89 |
| D, F | Mandelate RACEMASE/MUCONATE lactonizing enzyme | protein | 396 | 39% helix, 21% strand | Q1QT89 |
| E | Mandelate RACEMASE/MUCONATE lactonizing enzyme | protein | 397 | 39% helix, 21% strand | Q1QT89 |
Ligands and binding sites
- GCO · D-gluconic acid · ligand · 8 copies · chains A, B, C, E, D, H, F, G
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 825 | 0.89 | 0.93 | 122 | empty |
| 2 | 656 | 0.89 | 0.93 | 108 | empty |
| 3 | 110 | 0.78 | 0.97 | 42 | empty |
| 4 | 124 | 0.77 | 0.96 | 46 | empty |
| 5 | 97 | 0.76 | 0.97 | 34 | empty |
Interfaces
13 interfaces between chains.
- C–E · 2745 Ų buried · 41 hydrogen bonds · protein-protein
- A–B · 2744 Ų buried · 38 hydrogen bonds · protein-protein
- F–G · 2742 Ų buried · 39 hydrogen bonds · protein-protein
- D–H · 2731 Ų buried · 40 hydrogen bonds · protein-protein
- C–H · 1350 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 3QKE · Crystal structure of D-mannonate dehydratase from Chromohalobacter Salexigens complexed… · the same entry in another collection · chain H against H, TM-score 1.00
- Q1QT89 · AlphaFold monomer V2.0 prediction for D-galactonate dehydratase family member mand… · a predicted model of the same protein · chain F 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 Q1QT89
- Elsewhere: RCSB PDB 3QKE · PDBe 3QKE · UniProt Q1QT89
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