MolNFT v1 · #5270 · protein
E. COLI glucarate dehydratase bound to 4-deoxyglucarate
1ECQ: “E. COLI glucarate dehydratase bound to 4-deoxyglucarate”. X-ray diffraction, 2 ligands (DXG, MG), 12 pockets (best druggability 0.84). MolNFT v1 #5270 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1ECQ
- Type
- protein
- Length
- 1,771 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
- DXG, MG
- Pockets
- 12 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glucarate dehydratase (EC 4.2.1.40) | protein | 444 | 39% helix, 18% strand | P76637 |
| B, D | Glucarate dehydratase (EC 4.2.1.40) | protein | 442 | 40% helix, 17% strand | P76637 |
| C | Glucarate dehydratase (EC 4.2.1.40) | protein | 443 | 40% helix, 18% strand | P76637 |
Ligands and binding sites
- DXG · 4-deoxyglucarate · 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
12 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 862 | 0.84 | 0.86 | 118 | IPA |
| 2 | 1196 | 0.83 | 0.84 | 145 | IPA |
| 3 | 208 | 0.70 | 0.87 | 42 | empty |
| 4 | 161 | 0.70 | 0.89 | 31 | IPA |
| 5 | 219 | 0.68 | 0.85 | 36 | empty |
Interfaces
6 interfaces between chains.
- A–C · 1574 Ų buried · 29 hydrogen bonds · protein-protein
- B–D · 1522 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 667 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 662 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 397 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 1ECQ · E. COLI glucarate dehydratase bound to 4-deoxyglucarate · 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 1ECQ · PDBe 1ECQ · UniProt P76637
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