MolNFT v1 · #114576 · protein
The structure of diels-alderase PYRI4 in the biosynthetic pathway of pyrroindomycins
5BTU: “The structure of diels-alderase PYRI4 in the biosynthetic pathway of pyrroindomycins”. X-ray diffraction, 6 pockets (best druggability 0.70). MolNFT v1 #114576 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5BTU
- Type
- protein
- Length
- 324 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- PYRI4
- UniProt
- K7QVW7
- Pockets
- 6 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 17% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | PYRI4 | protein | 162 | 17% helix, 51% strand | K7QVW7 |
Ligands and binding sites
- PEG · Di(hydroxyethyl)ether · additive · 6 copies · chains A, B
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 196 | 0.70 | 0.88 | 39 | GOL |
| 2 | 256 | 0.64 | 0.81 | 37 | PEG |
| 3 | 272 | 0.63 | 0.80 | 36 | PEG |
| 4 | 58 | 0.41 | 0.82 | 12 | empty |
| 5 | 61 | 0.32 | 0.77 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1396 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 modified, 2 disulfide (engineered, disulfide).
Compared structures
- 5BTU · The structure of Diels-Alderase PyrI4 in the biosynthetic pathway of pyrroindomycins · the same entry in another collection · chain A against A, TM-score 1.00
- K7QVW7 · AlphaFold monomer V2.0 prediction for spiro-conjugate synthase (K7QVW7) · a predicted model of the same protein · chain A against A, TM-score 0.94
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 K7QVW7
- Elsewhere: RCSB PDB 5BTU · PDBe 5BTU · UniProt K7QVW7
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