MolNFT v1 · #171831 · protein

Olep-OLEANDOLIDE(DEO) in high salt crystallization conditions

6ZHZ · Cytochrome P-450: “Olep-OLEANDOLIDE(DEO) in high salt crystallization conditions”. X-ray diffraction, 3 ligands (HEM, QR8, NA), 20 pockets (best druggability 0.87). MolNFT v1 #171831 on GenesisL1: 3D structure, binding sites and…

PDB: 6ZHZ
Type: protein
Length: 2,374 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cytochrome P-450
UniProt: Q59819
Ligands: HEM, QR8, NA
Pockets: 20 · best druggability 0.87

Structure

x-ray diffraction · 3 distinct chains · 51% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Cytochrome P-450	protein	396	52% helix, 10% strand	Q59819
B	Cytochrome P-450	protein	397	51% helix, 10% strand	Q59819
D, E, F	Cytochrome P-450	protein	395	50% helix, 10% strand	Q59819

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · 6 copies · chains A, B, C, D, E, F
QR8 · (3~{R},4~{S},5~{R},6~{S},7~{S},9~{S},11~{R},12~{S}, 13~{R},14~{R})-3,5,7,9,11,13,14-heptamethyl-4,6,12-tris(oxidanyl)-1-oxacyclotetradecane-2,10-dione · ligand · 6 copies · chains A, B, C, D, E, F
NA · Sodium ion · metal · 5 copies · chains A, B, C, D, F
FMT · Formic acid · additive · 83 copies · chains A, B, C, F, D, E
GOL · Glycerol · additive · 15 copies · chains A, B, C, D, F
TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 3 copies · chains A, D, F

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	775	0.87	0.90	65	HEM, QR8, FMT
2	833	0.87	0.90	71	HEM, QR8, FMT
3	819	0.87	0.89	70	HEM, QR8, FMT
4	766	0.87	0.90	67	HEM, QR8, FMT
5	836	0.87	0.89	71	HEM, QR8, FMT

Interfaces

5 interfaces between chains.

D–E · 736 Å² buried · 10 hydrogen bonds · protein-protein
B–F · 680 Å² buried · 5 hydrogen bonds · protein-protein
B–C · 600 Å² buried · 12 hydrogen bonds · protein-protein
A–D · 539 Å² buried · 5 hydrogen bonds · protein-protein
C–E · 94 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

6ZHZ · OleP-oleandolide(DEO) in high salt crystallization conditions · 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 Q59819
Elsewhere: RCSB PDB 6ZHZ · PDBe 6ZHZ · UniProt Q59819

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