MolNFT v1 · #164050 · protein

Structure of saposin B in complex with atovaquone

6SLR · Prosaposin: “Structure of saposin B in complex with atovaquone”. X-ray diffraction, 1 ligand (AOQ), 2 pockets (best druggability 0.71). MolNFT v1 #164050 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6SLR
Type: protein
Length: 240 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Prosaposin
UniProt: P07602
Ligands: AOQ
Pockets: 2 · best druggability 0.71

Structure

x-ray diffraction · 3 distinct chains · 83% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Prosaposin	protein	79	85% helix, 0% strand	P07602
B	Prosaposin	protein	81	83% helix, 0% strand	P07602
C	Prosaposin	protein	80	81% helix, 0% strand	P07602

Ligands and binding sites

AOQ · 2-[trans-4-(4-chlorophenyl)cyclohexyl]-3-hydroxynaphthalene-1,4-dione · ligand · 2 copies · chains B, A, C
GOL · Glycerol · additive · 3 copies · chains B, A, C

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1191	0.71	0.74	63	empty
2	143	0.43	0.74	20	empty

Interfaces

1 interface between chains.

A–C · 994 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 9 disulfide (disulfide).

Compared structures

6SLR · Structure of saposin B in complex with atovaquone · the same entry in another collection · chain A against A, TM-score 1.00
P07602 · AlphaFold monomer V2.0 prediction for prosaposin (P07602) · a predicted model of the same protein · chain B against A, TM-score 0.91

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 P07602
Elsewhere: RCSB PDB 6SLR · PDBe 6SLR · UniProt P07602

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