Research workbench
Crystal structure of keto-deoxy-D-galactarate dehydratase complexed with pyruvate
Analyse Crystal structure of keto-deoxy-D-galactarate dehydratase complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HWN
- Type
- protein
- Length
- 1,221 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable 5-dehydro-4-deoxyglucarate dehydratase
- EC
- 4.2.1.41
- UniProt
- Q8UB77
- Ligands
- PYR
- Pockets
- 12 · best druggability 0.67
Structure
x-ray diffraction · 4 distinct chains · 52% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable 5-dehydro-4-deoxyglucarate dehydratase (EC 4.2.1.41) | protein | 303 | 52% helix, 13% strand | Q8UB77 |
| B | Probable 5-dehydro-4-deoxyglucarate dehydratase (EC 4.2.1.41) | protein | 310 | 52% helix, 13% strand | Q8UB77 |
| C | Probable 5-dehydro-4-deoxyglucarate dehydratase (EC 4.2.1.41) | protein | 307 | 51% helix, 13% strand | Q8UB77 |
| D | Probable 5-dehydro-4-deoxyglucarate dehydratase (EC 4.2.1.41) | protein | 301 | 52% helix, 13% strand | Q8UB77 |
Ligands and binding sites
- PYR · Pyruvic acid · ligand · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 12 copies · chains A, D, B, C
- FMT · Formic acid · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 311 | 0.67 | 0.81 | 45 | PYR, FMT |
| 2 | 354 | 0.66 | 0.80 | 47 | PYR, FMT |
| 3 | 215 | 0.65 | 0.83 | 33 | PYR, FMT |
| 4 | 305 | 0.64 | 0.80 | 38 | PYR, FMT |
| 5 | 90 | 0.39 | 0.76 | 18 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1649 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 1631 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 852 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 845 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5HWN · Crystal structure of keto-deoxy-D-galactarate dehydratase complexed with pyruvate · the same entry in another collection · chain D against D, TM-score 1.00
- Q8UB77 · AlphaFold monomer V2.0 prediction for probable 5-dehydro-4-deoxyglucarate dehydratase… · 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 Q8UB77
- Elsewhere: RCSB PDB 5HWN · PDBe 5HWN · UniProt Q8UB77
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