MolNFT v1 · #161662 · protein
Crystal structure of anubix (PADA1) in complex with FMN and dimethylallyl pyrophosphate
6QLG · Flavin prenyltransferase PAD1, mitochondrial: “Crystal structure of anubix (PADA1) in complex with FMN and dimethylallyl pyrophosphate”. X-ray diffraction, 3 ligands (DMA, FMN, PO4), 18 pockets (best druggability 0.87). MolNFT v1…
- PDB
- 6QLG
- Type
- protein
- Length
- 1,123 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Flavin prenyltransferase PAD1, mitochondrial
- EC
- 2.5.1.129
- UniProt
- A3F715
- Ligands
- DMA, FMN, PO4
- Pockets
- 18 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, B, D, E, F | Flavin prenyltransferase PAD1, mitochondrial (EC 2.5.1.129) | protein | 187 | 43% helix, 16% strand | A3F715 |
| A | Flavin prenyltransferase PAD1, mitochondrial (EC 2.5.1.129) | protein | 188 | 43% helix, 16% strand | A3F715 |
Ligands and binding sites
- DMA · Dimethylallyl diphosphate · ligand · 6 copies · chains C, A, E, B, D, F
- FMN · Flavin mononucleotide · ligand · 6 copies · chains C, A, B, E, D, F
- PO4 · Phosphate ion · ion · chains C
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains C, A, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1112 | 0.87 | 0.87 | 118 | DMA, FMN |
| 2 | 390 | 0.82 | 0.90 | 47 | FMN, DMA |
| 3 | 687 | 0.73 | 0.80 | 57 | empty |
| 4 | 56 | 0.72 | 0.98 | 18 | PEG |
| 5 | 62 | 0.71 | 0.97 | 18 | PEG |
Interfaces
10 interfaces between chains.
- C–A · 1922 Ų buried · 24 hydrogen bonds · protein-protein
- D–F · 1916 Ų buried · 24 hydrogen bonds · protein-protein
- A–E · 731 Ų buried · 12 hydrogen bonds · protein-protein
- E–F · 731 Ų buried · 12 hydrogen bonds · protein-protein
- C–B · 731 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 6QLG · Crystal structure of AnUbiX (PadA1) in complex with FMN and dimethylallyl pyrophosphate · the same entry in another collection · chain C against C, 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 A3F715
- Elsewhere: RCSB PDB 6QLG · PDBe 6QLG · UniProt A3F715
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