MolNFT v1 · #139475 · protein
The structure of diels-alderase PYRE3 in the biosynthetic pathway of pyrroindomycins
5XGV: “The structure of diels-alderase PYRE3 in the biosynthetic pathway of pyrroindomycins”. X-ray diffraction, 1 ligand (FAD), 8 pockets (best druggability 0.82). MolNFT v1 #139475 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5XGV
- Type
- protein
- Length
- 922 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- PYRE3
- UniProt
- K7QRJ5
- Ligands
- FAD
- Pockets
- 8 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | PYRE3 | protein | 461 | 33% helix, 27% strand | K7QRJ5 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1018 | 0.82 | 0.83 | 100 | FAD |
| 2 | 1166 | 0.82 | 0.83 | 114 | FAD |
| 3 | 354 | 0.60 | 0.77 | 50 | empty |
| 4 | 156 | 0.58 | 0.83 | 23 | empty |
| 5 | 178 | 0.57 | 0.81 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 556 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5XGV · The structure of Diels-Alderase PyrE3 in the biosynthetic pathway of pyrroindomycins · the same entry in another collection · chain A against A, TM-score 1.00
- K7QRJ5 · AlphaFold monomer V2.0 prediction for dialkyldecalin synthase (K7QRJ5) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 K7QRJ5
- Elsewhere: RCSB PDB 5XGV · PDBe 5XGV · UniProt K7QRJ5
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