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The crystal structure of pregilvocarcin in complex with gilr, an oxidoreductase that catalyzes the terminal step of gilvocarcin biosynthesis
Analyse The crystal structure of pregilvocarcin in complex with gilr, an oxidoreductase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PQB
- Type
- protein
- Length
- 1,969 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative oxidoreductase
- UniProt
- Q7X2G7
- Ligands
- FAD, VGP
- Pockets
- 13 · best druggability 0.88
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative oxidoreductase | protein | 492 | 33% helix, 24% strand | Q7X2G7 |
| B, C | Putative oxidoreductase | protein | 493 | 33% helix, 24% strand | Q7X2G7 |
| D | Putative oxidoreductase | protein | 491 | 33% helix, 24% strand | Q7X2G7 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- VGP · (1R)-1,4-anhydro-6-deoxy-1-[(6R)-8-ethenyl-1,6-dihydroxy-10,12-dimethoxy-6H-dibenzo[c,h]chromen-4-yl]-D-galactitol · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 745 | 0.88 | 0.91 | 101 | FAD, VGP |
| 2 | 730 | 0.88 | 0.91 | 97 | FAD, VGP |
| 3 | 696 | 0.87 | 0.91 | 90 | FAD, VGP |
| 4 | 671 | 0.87 | 0.91 | 92 | FAD, VGP |
| 5 | 638 | 0.86 | 0.91 | 74 | empty |
Interfaces
3 interfaces between chains.
- A–D · 1657 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 1641 Ų buried · 25 hydrogen bonds · protein-protein
- B–D · 339 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 7 cofactor (flavinylation).
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 Q7X2G7
- Elsewhere: RCSB PDB 3PQB · PDBe 3PQB · UniProt Q7X2G7
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