Research workbench
Crystal structure of yeast YNQ8, a fumarylacetoacetate hydrolase family protein
Analyse Crystal structure of yeast YNQ8, a fumarylacetoacetate hydrolase family protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1NKQ
- Type
- protein
- Length
- 1,466 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical 28.8 kda protein in PSD1-SKO1 intergenic region
- UniProt
- P53889
- Ligands
- CA, SO4
- Pockets
- 15 · best druggability 0.77
Structure
x-ray diffraction · 5 distinct chains · 21% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hypothetical 28.8 kda protein in PSD1-SKO1 intergenic region | protein | 247 | 21% helix, 34% strand | P53889 |
| B, D | Hypothetical 28.8 kda protein in PSD1-SKO1 intergenic region | protein | 244 | 21% helix, 35% strand | P53889 |
| C | Hypothetical 28.8 kda protein in PSD1-SKO1 intergenic region | protein | 245 | 22% helix, 35% strand | P53889 |
| E | Hypothetical 28.8 kda protein in PSD1-SKO1 intergenic region | protein | 246 | 22% helix, 35% strand | P53889 |
| F | Hypothetical 28.8 kda protein in PSD1-SKO1 intergenic region | protein | 240 | 19% helix, 35% strand | P53889 |
Ligands and binding sites
- CA · Calcium ion · metal · 6 copies · chains A, B, C, D, E, F
- SO4 · Sulfate ion · ion · 7 copies · chains A, D, B, F, C, E
- ACY · Acetic acid · additive · 12 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1199 | 0.77 | 0.79 | 134 | SO4 |
| 2 | 752 | 0.71 | 0.77 | 75 | empty |
| 3 | 170 | 0.65 | 0.86 | 38 | SO4 |
| 4 | 217 | 0.60 | 0.81 | 21 | empty |
| 5 | 230 | 0.60 | 0.80 | 23 | empty |
Interfaces
9 interfaces between chains.
- A–B · 1963 Ų buried · 38 hydrogen bonds · protein-protein
- C–D · 1955 Ų buried · 42 hydrogen bonds · protein-protein
- E–F · 1944 Ų buried · 38 hydrogen bonds · protein-protein
- B–F · 744 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 709 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 30 modified (engineered).
Compared structures
- 1NKQ · Crystal structure of yeast ynq8, a fumarylacetoacetate hydrolase family protein · the same entry in another collection · chain F against F, TM-score 1.00
- P53889 · AlphaFold monomer V2.0 prediction for uncharacterized mitochondrial hydrolase FMP41… · a predicted model of the same protein · chain F 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 P53889
- Elsewhere: RCSB PDB 1NKQ · PDBe 1NKQ · UniProt P53889
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