4V2O: Saposin B

Structure of saposin B in complex with chloroquine. Determined by X-ray diffraction at 2.13 Å resolution. Released 9 Dec 2015.

Method: X-ray diffraction
Resolution: 2.13 Å
Organism: HOMO SAPIENS
Chains: 3
Atoms: 2,040
Mol. weight: 27.93 kDa
Ligands: CLQ
Released: 9 Dec 2015

Explore 4V2O in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4V2O contains 16 α-helices and 0 β-strands across 3 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	2-20	19
α-helix	24-35	12
α-helix	36-39	4
α-helix	43-63	21
α-helix	67-74	8

Chain B: 6 helices, 0 β-strands

Element	Residues	Length
α-helix	-1-1	3
α-helix	3-20	18
α-helix	24-35	12
α-helix	36-39	4
α-helix	43-63	21
α-helix	67-74	8

Chain C: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	-1-20	22
α-helix	24-35	12
α-helix	36-38	3
α-helix	43-63	21
α-helix	67-74	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Saposin-B	A, B, C	protein	82	HOMO SAPIENS	P07602 (AlphaFold model)

Sequence of entity 1 (A, B, C), FASTA

>4V2O_1 SAPOSIN-B (chains A, B, C)
GASGDVCQDCIQMVTDIQTAVRTNSTFVQALVEHVKEECDRLGPGMADICKNYISQYSEI
AIQMMMHMQPKEICALVGFCDE

Ligands and cofactors

ID	Name	Formula	Copies
CLQ	N4-(7-chloro-quinolin-4-yl)-N1,N1-diethyl-pentane-1,4-diamine	C18 H26 Cl N3	2

Primary citation

The Lysosomal Protein Saposin B Binds Chloroquine. Huta, B.P., Mehlenbacher, M.R., Nie, Y. et al. ChemMedChem (2016) 11:277. DOI 10.1002/CMDC.201500494 · PubMed

Other PDB entries of the same protein (UniProt P07602 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3BQP 1.3 Å, Crystal Structure of Human Saposin D (orthorhombic)
9I63 1.65 Å, Synthetic Human Saposin D glycoprotein
4UEX 1.8 Å, Structure of human Saposin A at lysosomal pH
4DDJ 1.9 Å, Crystal structure of saposin A in complex with lauryldimethylamine-N-oxide (LDAO)
2DOB 2.0 Å, Crystal Structure of Human Saposin A
3BQQ 2.0 Å, Crystal Structure of Human Saposin D (triclinic)
2RB3 2.1 Å, Crystal Structure of Human Saposin D
1N69 2.2 Å, Crystal structure of human saposin B
6SLR 2.38 Å, Structure of saposin B in complex with atovaquone
2GTG 2.4 Å, Crystal Structure of Human Saposin C
2QYP 2.45 Å, Orthorhombic Crystal Structure of Human Saposin C Dimer in Open Conformation
2R0R 2.5 Å, Crystal Structure of Human Saposin D variant SapD K9E

Browse structure collections

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