MolNFT v1 · #146947 · protein
Crystal structure of the ligj hydratase E284Q mutant substrate complex with (3Z)-2-keto-4-carboxy-3-hexenedioate
6DXS · 4-oxalomesaconate hydratase: “Crystal structure of the ligj hydratase E284Q mutant substrate complex with…”. X-ray diffraction, 2 ligands (HJ7, ZN), 12 pockets (best druggability 0.71). MolNFT v1 #146947 on GenesisL1: 3D structure…
- PDB
- 6DXS
- Type
- protein
- Length
- 1,368 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
- HJ7, ZN
- Pockets
- 12 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | 4-oxalomesaconate hydratase (EC 4.2.1.83) | protein | 342 | 48% helix, 10% strand | G2IQQ5 |
Ligands and binding sites
- HJ7 · (2Z)-4-oxobut-2-ene-1,2,4-tricarboxylic acid · ligand · 4 copies · chains A, D, B, C
- 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
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 597 | 0.71 | 0.79 | 84 | empty |
| 2 | 360 | 0.65 | 0.80 | 48 | empty |
| 3 | 193 | 0.56 | 0.79 | 30 | HJ7 |
| 4 | 136 | 0.54 | 0.81 | 23 | empty |
| 5 | 100 | 0.53 | 0.84 | 22 | ZN, HJ7 |
Interfaces
4 interfaces between chains.
- A–D · 2255 Ų buried · 31 hydrogen bonds · protein-protein
- B–D · 580 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 423 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 178 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6DXS · Crystal structure of the LigJ hydratase E284Q mutant substrate complex with… · the same entry in another collection · chain A against A, 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 0.99
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 6DXS · PDBe 6DXS · UniProt G2IQQ5
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