Research workbench
X-ray structure of homo sapiens fumarylacetoacetate hydrolase domain containing protein 1 (FAHD1) in complex with inhibitor oxalate at 1.94A resolution.
Analyse X-ray structure of homo sapiens 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
- 6FOG
- Type
- protein
- Length
- 1,730 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acylpyruvase FAHD1, mitochondrial
- EC
- 3.7.1.5, 4.1.1.3
- UniProt
- Q6P587
- Ligands
- OXL, MG, CL
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 5 distinct chains · 25% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acylpyruvase FAHD1, mitochondrial (EC 3.7.1.5, 4.1.1.3) | protein | 218 | 25% helix, 36% strand | Q6P587 |
| G, B, H | Acylpyruvase FAHD1, mitochondrial (EC 3.7.1.5, 4.1.1.3) | protein | 217 | 25% helix, 36% strand | Q6P587 |
| F, D | Acylpyruvase FAHD1, mitochondrial (EC 3.7.1.5, 4.1.1.3) | protein | 215 | 25% helix, 37% strand | Q6P587 |
| C | Acylpyruvase FAHD1, mitochondrial (EC 3.7.1.5, 4.1.1.3) | protein | 216 | 25% helix, 37% strand | Q6P587 |
| E | Acylpyruvase FAHD1, mitochondrial (EC 3.7.1.5, 4.1.1.3) | protein | 215 | 25% helix, 37% strand | Q6P587 |
Ligands and binding sites
- OXL · Oxalate ion · ligand · 8 copies · chains A, G, F, D, B, C, H, E
- MG · Magnesium ion · metal · 12 copies · chains A, C, G, E, F, H, D, B
- CL · Chloride ion · ion · 4 copies · chains A, C, F, H, D, B, G, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 735 | 0.79 | 0.83 | 83 | empty |
| 2 | 686 | 0.72 | 0.79 | 58 | empty |
| 3 | 56 | 0.70 | 0.98 | 20 | MG, OXL |
| 4 | 52 | 0.69 | 0.97 | 20 | OXL |
| 5 | 60 | 0.67 | 0.95 | 20 | OXL |
Interfaces
13 interfaces between chains.
- A–C · 1431 Ų buried · 23 hydrogen bonds · protein-protein
- F–H · 1379 Ų buried · 22 hydrogen bonds · protein-protein
- D–B · 1355 Ų buried · 21 hydrogen bonds · protein-protein
- G–E · 1350 Ų buried · 20 hydrogen bonds · protein-protein
- F–C · 565 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6FOG · X-ray structure of homo sapiens Fumarylacetoacetate hydrolase domain containing protein 1… · the same entry in another collection · chain E against E, TM-score 1.00
- Q6P587 · AlphaFold monomer V2.0 prediction for acylpyruvase FAHD1, mitochondrial (Q6P587) · a predicted model of the same protein · chain E 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 Q6P587
- Elsewhere: RCSB PDB 6FOG · PDBe 6FOG · UniProt Q6P587
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.