Research workbench
Structure of P450 StaH from glycopeptide antibiotic A47934 biosynthesis
Analyse Structure of P450 StaH from glycopeptide antibiotic A47934 biosynthesis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5EX6
- Type
- protein
- Length
- 1,145 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.4
- Source
- Streptomyces toyocaensis
- Molecule
- Cytochrome P450
- UniProt
- Q8KLL9
- Ligands
- HEM
- Pockets
- 14 · best druggability 0.82
Structure
x-ray diffraction · resolution 2.4 · 3 distinct chains · 51% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Cytochrome P450 | protein | 388 | 51% helix, 12% strand | Q8KLL9 |
| A | Cytochrome P450 | protein | 386 | 51% helix, 12% strand | Q8KLL9 |
| B | Cytochrome P450 | protein | 371 | 52% helix, 11% strand | Q8KLL9 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 3 copies · chains C, A, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains C, A
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 451 | 0.82 | 0.89 | 50 | GOL, HEM |
| 2 | 738 | 0.81 | 0.85 | 82 | GOL, EDO, HEM |
| 3 | 1035 | 0.80 | 0.81 | 75 | empty |
| 4 | 655 | 0.79 | 0.84 | 62 | empty |
| 5 | 1155 | 0.79 | 0.80 | 109 | EDO, HEM |
Interfaces
3 interfaces between chains.
- A–B · 1167 Ų buried · 22 hydrogen bonds · protein-protein
- C–A · 802 Ų buried · 14 hydrogen bonds · protein-protein
- C–B · 159 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5EX6 · Structure of P450 stah from glycopeptide antibiotic A47934 biosynthesis · the same entry in another collection · chain A 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 Q8KLL9
- Elsewhere: RCSB PDB 5EX6 · PDBe 5EX6 · UniProt Q8KLL9
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