Research workbench
Structure of putative glucarate dehydratase from acidaminococcus sp. D21 with unusual static disorder
Analyse Structure of putative glucarate dehydratase from acidaminococcus sp. D21 with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HYR
- Type
- protein
- Length
- 873 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucarate dehydratase
- UniProt
- C0WBB5
- Ligands
- CL
- Pockets
- 4 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glucarate dehydratase | protein | 442 | 39% helix, 18% strand | C0WBB5 |
| B | Glucarate dehydratase | protein | 431 | 41% helix, 19% strand | C0WBB5 |
Ligands and binding sites
- CL · Chloride ion · ion · 3 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1170 | 0.80 | 0.82 | 112 | EDO, CL |
| 2 | 255 | 0.69 | 0.85 | 33 | empty |
| 3 | 72 | 0.42 | 0.80 | 21 | empty |
| 4 | 113 | 0.40 | 0.76 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1405 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 modified (engineered).
Compared structures
- 4HYR · Structure of putative Glucarate dehydratase from Acidaminococcus sp. D21 with unusual… · the same entry in another collection · 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 C0WBB5
- Elsewhere: RCSB PDB 4HYR · PDBe 4HYR · UniProt C0WBB5
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