Research workbench
Crystal structure of D-mannonate dehydratase from chromohalobacter salexigens complexed with MG,D-mannonate and 2-keto-3-deoxy-D- gluconate
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
- 4KPL
- Type
- protein
- Length
- 3,086 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
- CS2, KDG, MG, CL
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 7 distinct chains · 39% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, H | D-mannonate dehydratase (EC 4.2.1.8) | protein | 384 | 40% helix, 21% strand | Q1QT89 |
| B | D-mannonate dehydratase (EC 4.2.1.8) | protein | 390 | 39% helix, 21% strand | Q1QT89 |
| C | D-mannonate dehydratase (EC 4.2.1.8) | protein | 385 | 39% helix, 20% strand | Q1QT89 |
| D | D-mannonate dehydratase (EC 4.2.1.8) | protein | 384 | 40% helix, 20% strand | Q1QT89 |
| E | D-mannonate dehydratase (EC 4.2.1.8) | protein | 389 | 39% helix, 20% strand | Q1QT89 |
| F | D-mannonate dehydratase (EC 4.2.1.8) | protein | 387 | 40% helix, 20% strand | Q1QT89 |
| G | D-mannonate dehydratase (EC 4.2.1.8) | protein | 383 | 40% helix, 20% strand | Q1QT89 |
Ligands and binding sites
- CS2 · D-mannonic acid · ligand · 4 copies · chains A, E, B, D, F, H
- KDG · 2-keto-3-deoxygluconate · ligand · 4 copies · chains C, G, B, D, F, H
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
- CL · Chloride ion · ion · 4 copies · chains A, E, C, G, B, D, F, H
- GOL · Glycerol · additive · chains C, 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 | 604 | 0.87 | 0.92 | 99 | empty |
| 2 | 616 | 0.86 | 0.91 | 89 | GOL |
| 3 | 619 | 0.86 | 0.91 | 90 | empty |
| 4 | 628 | 0.86 | 0.90 | 92 | empty |
| 5 | 625 | 0.85 | 0.90 | 96 | empty |
Interfaces
16 interfaces between chains.
- C–G · 2750 Ų buried · 38 hydrogen bonds · protein-protein
- B–D · 2746 Ų buried · 39 hydrogen bonds · protein-protein
- A–E · 2735 Ų buried · 37 hydrogen bonds · protein-protein
- F–H · 2718 Ų buried · 37 hydrogen bonds · protein-protein
- A–G · 1378 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 4KPL · 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 D 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 4KPL · PDBe 4KPL · UniProt Q1QT89
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