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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
- 4KT2
- Type
- protein
- Length
- 3,100 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, SO4, CL
- Pockets
- 20 · best druggability 0.88
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 | 384 | 40% helix, 20% strand | Q1QT89 |
| B | D-mannonate dehydratase (EC 4.2.1.8) | protein | 391 | 39% helix, 20% strand | Q1QT89 |
| C | D-mannonate dehydratase (EC 4.2.1.8) | protein | 385 | 40% helix, 20% strand | Q1QT89 |
| D, G | D-mannonate dehydratase (EC 4.2.1.8) | protein | 385 | 40% helix, 20% strand | Q1QT89 |
| E | D-mannonate dehydratase (EC 4.2.1.8) | protein | 395 | 39% helix, 20% strand | Q1QT89 |
| F | D-mannonate dehydratase (EC 4.2.1.8) | protein | 387 | 40% helix, 20% strand | Q1QT89 |
| H | D-mannonate dehydratase (EC 4.2.1.8) | protein | 388 | 39% helix, 21% 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 · 14 copies · chains A, B, C, D, E, F, G, H
- CL · Chloride ion · ion · 4 copies · chains A, E, B, D, C, G, F, H
- GOL · Glycerol · additive · 9 copies · chains A, E, B, D, C, G, F, 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 | 477 | 0.88 | 0.96 | 73 | empty |
| 2 | 606 | 0.86 | 0.91 | 86 | empty |
| 3 | 419 | 0.84 | 0.92 | 60 | empty |
| 4 | 230 | 0.83 | 0.96 | 35 | empty |
| 5 | 240 | 0.82 | 0.95 | 44 | empty |
Interfaces
16 interfaces between chains.
- F–H · 2752 Ų buried · 37 hydrogen bonds · protein-protein
- C–G · 2739 Ų buried · 35 hydrogen bonds · protein-protein
- A–E · 2739 Ų buried · 35 hydrogen bonds · protein-protein
- B–D · 2715 Ų buried · 35 hydrogen bonds · protein-protein
- A–G · 1402 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 4KT2 · Crystal structure of d-mannonate dehydratase from chromohalobacter salexigens complexed… · the same entry in another collection · chain F against F, 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 C 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 4KT2 · PDBe 4KT2 · UniProt Q1QT89
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