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Crystal structure of the yc-17-bound pikc D50N mutant

Analyse Crystal structure of the yc-17-bound pikc D50N mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2VZ7
Type: protein
Length: 789 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cytochrome P450 monooxygenase
UniProt: O87605
Ligands: HEM, PXI
Pockets: 6 · best druggability 0.86

Structure

x-ray diffraction · 2 distinct chains · 53% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cytochrome P450 monooxygenase	protein	396	51% helix, 10% strand	O87605
B	Cytochrome P450 monooxygenase	protein	393	55% helix, 10% strand	O87605

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
PXI · 4-{[4-(dimethylamino)-3-hydroxy-6-methyltetrahydro-2H-pyran-2-yl]oxy}-12-ethyl-3,5,7,11-tetramethyloxacyclododec-9-ene-2,8-dione · ligand · 2 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, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1023	0.86	0.86	81	HEM, PXI
2	1068	0.86	0.86	84	HEM, PXI
3	779	0.72	0.78	61	empty
4	67	0.58	0.89	16	empty
5	121	0.40	0.75	23	empty

Interfaces

1 interface between chains.

A–B · 436 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

2VZ7 · Crystal structure of the YC-17-bound PikC D50N mutant · the same entry in another collection · chain A against A, TM-score 1.00
O87605 · AlphaFold monomer V2.0 prediction for cytochrome P450 monooxygenase pikc (O87605) · a predicted model of the same protein · chain B against A, TM-score 0.99

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 O87605
Elsewhere: RCSB PDB 2VZ7 · PDBe 2VZ7 · UniProt O87605

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