Research workbench
Crystal structure of D-mannonate dehydratase from chromohalobacter salexigens complexed with mg and glycerol
Analyse Crystal structure of D-mannonate dehydratase from chromohalobacter salexigens… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KWS
- Type
- protein
- Length
- 3,164 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-mannonate dehydratase
- EC
- 4.2.1.8
- UniProt
- Q1QT89
- Ligands
- MG, CL
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 7 distinct chains · 39% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-mannonate dehydratase (EC 4.2.1.8) | protein | 397 | 39% helix, 20% strand | Q1QT89 |
| B | D-mannonate dehydratase (EC 4.2.1.8) | protein | 393 | 39% helix, 20% strand | Q1QT89 |
| C | D-mannonate dehydratase (EC 4.2.1.8) | protein | 397 | 39% helix, 20% strand | Q1QT89 |
| D | D-mannonate dehydratase (EC 4.2.1.8) | protein | 395 | 39% helix, 20% strand | Q1QT89 |
| E, G | D-mannonate dehydratase (EC 4.2.1.8) | protein | 396 | 39% helix, 20% strand | Q1QT89 |
| F | D-mannonate dehydratase (EC 4.2.1.8) | protein | 395 | 39% helix, 20% strand | Q1QT89 |
| H | D-mannonate dehydratase (EC 4.2.1.8) | protein | 395 | 38% helix, 20% strand | Q1QT89 |
Ligands and binding sites
- MG · Magnesium ion · metal · 13 copies · chains A, F, B, G, C, E, D, H
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D, E, H, F, G
- GOL · Glycerol · additive · 8 copies · chains A, B, C, D, E, H, F, G
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 | 655 | 0.89 | 0.94 | 99 | empty |
| 2 | 573 | 0.86 | 0.91 | 95 | empty |
| 3 | 406 | 0.84 | 0.92 | 59 | empty |
| 4 | 115 | 0.78 | 0.97 | 41 | empty |
| 5 | 109 | 0.77 | 0.97 | 38 | empty |
Interfaces
14 interfaces between chains.
- F–G · 2752 Ų buried · 37 hydrogen bonds · protein-protein
- A–B · 2747 Ų buried · 41 hydrogen bonds · protein-protein
- E–H · 2746 Ų buried · 42 hydrogen bonds · protein-protein
- C–D · 2720 Ų buried · 34 hydrogen bonds · protein-protein
- B–F · 1395 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 4KWS · 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 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 Q1QT89
- Elsewhere: RCSB PDB 4KWS · PDBe 4KWS · UniProt Q1QT89
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