MolNFT v1 · #146916 · protein
Crystal structure of the ligj hydratase in the apo state
6DWV · 4-oxalomesaconate hydratase: “Crystal structure of the ligj hydratase in the apo state”. X-ray diffraction, 1 ligand (ZN), 12 pockets (best druggability 0.80). MolNFT v1 #146916 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 6DWV
- Type
- protein
- Length
- 1,356 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
- ZN
- Pockets
- 12 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A, C, D | 4-oxalomesaconate hydratase (EC 4.2.1.83) | protein | 339 | 48% helix, 11% strand | G2IQQ5 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains B, A, 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 898 | 0.80 | 0.82 | 70 | empty |
| 2 | 70 | 0.72 | 0.97 | 23 | empty |
| 3 | 135 | 0.46 | 0.77 | 31 | empty |
| 4 | 133 | 0.45 | 0.76 | 22 | empty |
| 5 | 76 | 0.41 | 0.79 | 19 | ZN |
Interfaces
3 interfaces between chains.
- B–C · 2322 Ų buried · 30 hydrogen bonds · protein-protein
- A–C · 791 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 333 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6DWV · Crystal structure of the LigJ Hydratase in the Apo state · the same entry in another collection · chain B against B, 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 B 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 6DWV · PDBe 6DWV · UniProt G2IQQ5
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