Research workbench
X-ray structure of murine fumarylacetoacetate hydrolase domain containing protein 1 (FAHD1) in complex with inhibitor oxalate
Analyse X-ray structure of murine fumarylacetoacetate hydrolase domain containing… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6SBI
- Type
- protein
- Length
- 862 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acylpyruvase FAHD1, mitochondrial
- EC
- 3.7.1.5, 4.1.1.112
- UniProt
- Q8R0F8
- Ligands
- OXL, MG, K, CL
- Pockets
- 16 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 22% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Acylpyruvase FAHD1, mitochondrial (EC 3.7.1.5, 4.1.1.112) | protein | 216 | 22% helix, 37% strand | Q8R0F8 |
| C | Acylpyruvase FAHD1, mitochondrial (EC 3.7.1.5, 4.1.1.112) | protein | 214 | 22% helix, 37% strand | Q8R0F8 |
Ligands and binding sites
- OXL · Oxalate ion · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- K · Potassium ion · metal · 2 copies · chains A, B, C, D
- CL · Chloride ion · ion · 9 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 822 | 0.75 | 0.79 | 77 | CL |
| 2 | 63 | 0.69 | 0.96 | 20 | MG, OXL |
| 3 | 56 | 0.69 | 0.97 | 21 | MG, OXL |
| 4 | 59 | 0.62 | 0.92 | 21 | MG, OXL |
| 5 | 90 | 0.61 | 0.88 | 24 | MG, OXL |
Interfaces
4 interfaces between chains.
- C–D · 1384 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1354 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 290 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 81 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6SBI · X-ray structure of murine Fumarylacetoacetate hydrolase domain containing protein 1… · the same entry in another collection · chain D against D, TM-score 1.00
- Q8R0F8 · AlphaFold monomer V2.0 prediction for acylpyruvase FAHD1, mitochondrial (Q8R0F8) · a predicted model of the same protein · chain C 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 Q8R0F8
- Elsewhere: RCSB PDB 6SBI · PDBe 6SBI · UniProt Q8R0F8
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