MolNFT v1 · #171832 · protein

Olep-OLEANDOLIDE(DEO) in low salt crystallization conditions

6ZI2 · Cytochrome P-450: “Olep-OLEANDOLIDE(DEO) in low salt crystallization conditions”. X-ray diffraction, 2 ligands (HEM, QR8), 20 pockets (best druggability 0.88). MolNFT v1 #171832 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 6ZI2
Type: protein
Length: 3,382 residues
Chains: 9
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cytochrome P-450
UniProt: Q59819
Ligands: HEM, QR8
Pockets: 20 · best druggability 0.88

Structure

x-ray diffraction · 5 distinct chains · 53% helix, 9% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D, F	Cytochrome P-450	protein	394	51% helix, 9% strand	Q59819
B, C, H	Cytochrome P-450	protein	395	51% helix, 9% strand	Q59819
E	Cytochrome P-450	protein	386	51% helix, 10% strand	Q59819
G	Cytochrome P-450	protein	381	51% helix, 10% strand	Q59819
I	Cytochrome P-450	protein	248	65% helix, 5% strand	Q59819

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · 9 copies · chains A, B, C, D, E, F, G, H, I
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 · 9 copies · chains A, B, C, D, E, F, G, H, I

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

Pockets

20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	801	0.88	0.90	67	HEM, QR8
2	816	0.87	0.89	67	HEM, QR8
3	789	0.81	0.84	66	HEM, QR8
4	1036	0.81	0.82	95	HEM, QR8
5	1016	0.81	0.82	71	HEM, QR8

Interfaces

14 interfaces between chains.

D–F · 624 Å² buried · 10 hydrogen bonds · protein-protein
A–H · 610 Å² buried · 10 hydrogen bonds · protein-protein
C–E · 602 Å² buried · 9 hydrogen bonds · protein-protein
B–G · 590 Å² buried · 8 hydrogen bonds · protein-protein
B–D · 578 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

6ZI2 · OleP-oleandolide(DEO) in low 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 6ZI2 · PDBe 6ZI2 · UniProt Q59819

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