MolNFT v1 · #187507 · protein
Crystal structure of cytochrome P450 amphl from streptomyces nodosus and the structural basis for substrate selectivity in macrolide metabolizing P450S
7SHI: “Crystal structure of cytochrome P450 amphl from streptomyces nodosus and the structural basis for substrate…”. X-ray diffraction, 3 ligands (HEM, 4UH, SO4), 6 pockets (best druggability 0.86). MolNFT v1 #187507 on GenesisL1: 3D…
- 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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