MolNFT v1 · #146945 · protein
Crystal structure of the ligj hydratase product complex with 4- carboxy-4-hydroxy-2-oxoadipate
6DXQ · 4-oxalomesaconate hydratase: “Crystal structure of the ligj hydratase product complex with 4- carboxy-4-hydroxy-2-oxoadipate”. X-ray diffraction, 2 ligands (7QD, ZN), 10 pockets (best druggability 0.69). MolNFT v1 #146945 on…
- PDB
- 6DXQ
- Type
- protein
- Length
- 1,342 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 4-oxalomesaconate hydratase
- EC
- 4.2.1.83
- UniProt
- G2IQQ5
- Ligands
- 7QD, ZN
- Pockets
- 10 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 49% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 4-oxalomesaconate hydratase (EC 4.2.1.83) | protein | 338 | 49% helix, 12% strand | G2IQQ5 |
| B | 4-oxalomesaconate hydratase (EC 4.2.1.83) | protein | 338 | 48% helix, 11% strand | G2IQQ5 |
| C | 4-oxalomesaconate hydratase (EC 4.2.1.83) | protein | 334 | 50% helix, 11% strand | G2IQQ5 |
| D | 4-oxalomesaconate hydratase (EC 4.2.1.83) | protein | 332 | 48% helix, 11% strand | G2IQQ5 |
Ligands and binding sites
- 7QD · (2S)-2-hydroxy-4-oxobutane-1,2,4-tricarboxylic acid · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 672 | 0.69 | 0.77 | 61 | empty |
| 2 | 414 | 0.65 | 0.79 | 52 | empty |
| 3 | 166 | 0.54 | 0.79 | 31 | 7QD |
| 4 | 174 | 0.52 | 0.78 | 30 | ZN, 7QD |
| 5 | 156 | 0.51 | 0.78 | 31 | 7QD |
Interfaces
2 interfaces between chains.
- B–D · 476 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 341 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6DXQ · Crystal structure of the LigJ Hydratase product complex with… · the same entry in another collection · chain D against D, TM-score 1.00
- G2IQQ5 · AlphaFold monomer V2.0 prediction for 2-keto-4-carboxy-3-hexenedioate hydratase (G2IQQ5) · a predicted model of the same protein · 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 G2IQQ5
- Elsewhere: RCSB PDB 6DXQ · PDBe 6DXQ · UniProt G2IQQ5
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