Research workbench
Crystal structure of a putative D-glucarate dehydratase from pseudomonas mendocina ymp
Analyse Crystal structure of a putative D-glucarate dehydratase from pseudomonas… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HN8
- Type
- protein
- Length
- 3,412 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-glucarate dehydratase
- EC
- 4.2.1.40
- UniProt
- A4XRL3
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, H | D-glucarate dehydratase (EC 4.2.1.40) | protein | 427 | 41% helix, 19% strand | A4XRL3 |
| B, E, F, G | D-glucarate dehydratase (EC 4.2.1.40) | protein | 426 | 40% helix, 19% strand | A4XRL3 |
Ligands and binding sites
- GOL · Glycerol · additive · 9 copies · chains A, B, C, D, E, F, G, 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 | 117 | 0.76 | 0.96 | 23 | empty |
| 2 | 101 | 0.74 | 0.95 | 25 | empty |
| 3 | 88 | 0.73 | 0.96 | 22 | empty |
| 4 | 886 | 0.71 | 0.76 | 78 | GOL |
| 5 | 924 | 0.71 | 0.76 | 103 | empty |
Interfaces
15 interfaces between chains.
- F–H · 1611 Ų buried · 17 hydrogen bonds · protein-protein
- E–G · 1592 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 1589 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 1568 Ų buried · 18 hydrogen bonds · protein-protein
- E–F · 762 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 112 modified (engineered).
Compared structures
- 4HN8 · Crystal structure of a putative D-glucarate dehydratase from Pseudomonas mendocina ymp · 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 A4XRL3
- Elsewhere: RCSB PDB 4HN8 · PDBe 4HN8 · UniProt A4XRL3
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