MolNFT v1 · #74410 · protein
Crystal structure of D-mannonate dehydratase from chromohalobacter salexigens complexed with mg
3OW1 · Mandelate RACEMASE/MUCONATE lactonizing enzyme: “Crystal structure of D-mannonate dehydratase from chromohalobacter salexigens complexed with mg”. X-ray diffraction, 2 ligands (MG, SO4), 20 pockets (best druggability 0.89). MolNFT…
- PDB
- 3OW1
- Type
- protein
- Length
- 3,092 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mandelate RACEMASE/MUCONATE lactonizing enzyme
- UniProt
- Q1QT89
- Ligands
- MG, SO4
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 5 distinct chains · 40% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mandelate RACEMASE/MUCONATE lactonizing enzyme | protein | 384 | 40% helix, 20% strand | Q1QT89 |
| B | Mandelate RACEMASE/MUCONATE lactonizing enzyme | protein | 388 | 39% helix, 20% strand | Q1QT89 |
| C, D, F, H | Mandelate RACEMASE/MUCONATE lactonizing enzyme | protein | 387 | 40% helix, 20% strand | Q1QT89 |
| E | Mandelate RACEMASE/MUCONATE lactonizing enzyme | protein | 389 | 39% helix, 20% strand | Q1QT89 |
| G | Mandelate RACEMASE/MUCONATE lactonizing enzyme | protein | 383 | 40% helix, 20% strand | Q1QT89 |
Ligands and binding sites
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
- SO4 · Sulfate ion · ion · 15 copies · chains A, B, C, D, E, F, G, H
- GOL · Glycerol · additive · 11 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 | 845 | 0.89 | 0.92 | 119 | empty |
| 2 | 875 | 0.89 | 0.92 | 127 | empty |
| 3 | 879 | 0.89 | 0.92 | 123 | empty |
| 4 | 612 | 0.85 | 0.90 | 84 | empty |
| 5 | 444 | 0.85 | 0.92 | 67 | empty |
Interfaces
16 interfaces between chains.
- E–F · 2754 Ų buried · 36 hydrogen bonds · protein-protein
- C–D · 2752 Ų buried · 37 hydrogen bonds · protein-protein
- G–H · 2739 Ų buried · 35 hydrogen bonds · protein-protein
- A–B · 2734 Ų buried · 35 hydrogen bonds · protein-protein
- D–E · 1349 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 3OW1 · 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 3OW1 · PDBe 3OW1 · UniProt Q1QT89
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