Research workbench
E. COLI glucarate dehydratase bound to xylarohydroxamate
Analyse E. COLI glucarate dehydratase bound to xylarohydroxamate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1EC9
- Type
- protein
- Length
- 1,773 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucarate dehydratase
- EC
- 4.2.1.40
- UniProt
- P76637
- Ligands
- XYH, MG
- Pockets
- 15 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Glucarate dehydratase (EC 4.2.1.40) | protein | 443 | 39% helix, 18% strand | P76637 |
| D | Glucarate dehydratase (EC 4.2.1.40) | protein | 444 | 39% helix, 18% strand | P76637 |
Ligands and binding sites
- XYH · Xylarohydroxamate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- IPA · Isopropyl alcohol · additive · 4 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 588 | 0.80 | 0.86 | 87 | empty |
| 2 | 523 | 0.80 | 0.86 | 72 | empty |
| 3 | 297 | 0.78 | 0.90 | 43 | IPA |
| 4 | 339 | 0.78 | 0.88 | 56 | IPA |
| 5 | 230 | 0.68 | 0.85 | 34 | empty |
Interfaces
6 interfaces between chains.
- A–C · 1607 Ų buried · 28 hydrogen bonds · protein-protein
- B–D · 1596 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 666 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 660 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 397 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 1EC9 · E. COLI glucarate dehydratase bound to xylarohydroxamate · 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 P76637
- Elsewhere: RCSB PDB 1EC9 · PDBe 1EC9 · UniProt P76637
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