MolNFT v1 · #11128 · protein
Glucarate dehydratase from E.COLI N341D mutant
1JDF: “Glucarate dehydratase from E.COLI N341D mutant”. X-ray diffraction, 2 ligands (GLR, MG), 14 pockets (best druggability 0.83). MolNFT v1 #11128 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1JDF
- Type
- protein
- Length
- 1,768 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
- GLR, MG
- Pockets
- 14 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Glucarate dehydratase (EC 4.2.1.40) | protein | 442 | 40% helix, 17% strand | P76637 |
Ligands and binding sites
- GLR · 2,3-dihydroxy-5-oxo-hexanedioate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- IPA · Isopropyl alcohol · additive · 8 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 798 | 0.83 | 0.86 | 105 | IPA |
| 2 | 981 | 0.81 | 0.83 | 115 | IPA |
| 3 | 308 | 0.76 | 0.88 | 52 | IPA |
| 4 | 217 | 0.69 | 0.86 | 34 | empty |
| 5 | 197 | 0.69 | 0.87 | 36 | empty |
Interfaces
6 interfaces between chains.
- B–D · 1577 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 1566 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 677 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 677 Ų buried · 21 hydrogen bonds · protein-protein
- A–D · 409 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 1JDF · Glucarate Dehydratase from E.coli N341D mutant · 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 1JDF · PDBe 1JDF · UniProt P76637
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