MolNFT v1 · #86318 · protein

Structure of OSH6 in complex with phosphatidylserine

4B2Z · Oxysterol-binding protein homolog 6: “Structure of OSH6 in complex with phosphatidylserine”. X-ray diffraction, 2 ligands (P5S, SO4), 12 pockets (best druggability 0.87). MolNFT v1 #86318 on GenesisL1: 3D structure, binding sites…

PDB: 4B2Z
Type: protein
Length: 799 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Oxysterol-binding protein homolog 6
UniProt: Q02201
Ligands: P5S, SO4
Pockets: 12 · best druggability 0.87

Structure

x-ray diffraction · 2 distinct chains · 27% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Oxysterol-binding protein homolog 6	protein	399	28% helix, 30% strand	Q02201
B	Oxysterol-binding protein homolog 6	protein	400	26% helix, 30% strand	Q02201

Ligands and binding sites

P5S · O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy) propyl]oxy}(hydroxy)phosphoryl]-L-serine · ligand · 2 copies · chains A, B
SO4 · Sulfate ion · ion · 2 copies · chains A, B
DTU · (2R,3S)-1,4-dimercaptobutane-2,3-diol · additive · chains A
DTT · 2,3-dihydroxy-1,4-dithiobutane · additive · chains A, B

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

Pockets

12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1031	0.87	0.88	103	DTT
2	643	0.87	0.91	70	P5S
3	692	0.86	0.89	70	SO4, P5S
4	88	0.50	0.83	19	empty
5	108	0.48	0.80	21	empty

Interfaces

1 interface between chains.

A–B · 1831 Å² buried · 25 hydrogen bonds · protein-protein

Compared structures

4B2Z · Structure of Osh6 in complex with phosphatidylserine · the same entry in another collection · chain B against B, TM-score 1.00
Q02201 · AlphaFold monomer V2.0 prediction for oxysterol-binding protein homolog 6 (Q02201) · a predicted model of the same protein · chain A 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 Q02201
Elsewhere: RCSB PDB 4B2Z · PDBe 4B2Z · UniProt Q02201

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