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Crystal structure of cytochrome P450 amphl from streptomyces nodosus and the structural basis for substrate selectivity in macrolide metabolizing P450S
Analyse Crystal structure of cytochrome P450 amphl from streptomyces nodosus and the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7SHI
- Type
- protein
- Length
- 782 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Amphl
- UniProt
- Q93NX6
- Ligands
- HEM, 4UH, SO4
- Pockets
- 6 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 52% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Amphl | protein | 391 | 52% helix, 11% strand | Q93NX6 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- 4UH · (1R,3S,5R,6R,9R,11R,15S,16R,17R,18S,19E,22E,33S,35S, 36R,37S)-33-[(3-amino-3,6-dideoxy-beta-D-mannopyranosyl)oxy]-1,3,5,6,9,11,17,37-octahydroxy-15, 16,18-trimethyl-13-oxo-14,39-dioxabicyclo[33.3.1]nonatriaconta-19,22-diene-36-carboxylic acid · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · 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 | 681 | 0.86 | 0.90 | 79 | HEM, 4UH |
| 2 | 591 | 0.85 | 0.90 | 83 | HEM, 4UH |
| 3 | 183 | 0.74 | 0.90 | 30 | empty |
| 4 | 57 | 0.31 | 0.76 | 15 | empty |
| 5 | 73 | 0.30 | 0.73 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 638 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 7SHI · Crystal Structure of Cytochrome P450 AmphL from Streptomyces nodosus and the Structural… · 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 Q93NX6
- Elsewhere: RCSB PDB 7SHI · PDBe 7SHI · UniProt Q93NX6
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