Research workbench
2.75 ångström crystal structure of galactarate dehydratase from escherichia COLI.
Analyse 2.75 ångström crystal structure of galactarate dehydratase from escherichia… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6U7L
- Type
- protein
- Length
- 1,816 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Galactarate dehydratase (L-threo-forming)
- EC
- 4.2.1.42
- UniProt
- P39829
- Ligands
- CA, CL
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Galactarate dehydratase (L-threo-forming) (EC 4.2.1.42) | protein | 460 | 33% helix, 18% strand | P39829 |
| B | Galactarate dehydratase (L-threo-forming) (EC 4.2.1.42) | protein | 451 | 33% helix, 19% strand | P39829 |
| C | Galactarate dehydratase (L-threo-forming) (EC 4.2.1.42) | protein | 453 | 34% helix, 19% strand | P39829 |
| D | Galactarate dehydratase (L-threo-forming) (EC 4.2.1.42) | protein | 452 | 33% helix, 19% strand | P39829 |
Ligands and binding sites
- CA · Calcium ion · metal · 9 copies · chains A, D, B, C
- CL · Chloride ion · ion · 7 copies · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 964 | 0.86 | 0.87 | 107 | empty |
| 2 | 822 | 0.85 | 0.88 | 88 | empty |
| 3 | 546 | 0.83 | 0.89 | 77 | empty |
| 4 | 511 | 0.81 | 0.87 | 68 | empty |
| 5 | 332 | 0.61 | 0.77 | 33 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2043 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 2035 Ų buried · 29 hydrogen bonds · protein-protein
- A–C · 666 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 462 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 132 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 38 modified (engineered, phosphorylation).
Compared structures
- 6U7L · 2.75 Angstrom Crystal Structure of Galactarate Dehydratase from Escherichia coli. · the same entry in another collection · chain D against D, TM-score 1.00
- P39829 · AlphaFold monomer V2.0 prediction for galactarate dehydratase (L-threo-forming) (P39829) · a predicted model of the same protein · chain C against A, TM-score 0.95
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 P39829
- Elsewhere: RCSB PDB 6U7L · PDBe 6U7L · UniProt P39829
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