3BQP: Human Saposin D

Crystal Structure of Human Saposin D (orthorhombic). Determined by X-ray diffraction at 1.3 Å resolution. Released 5 Feb 2008.

Method: X-ray diffraction
Resolution: 1.3 Å
Organism: Homo sapiens
Chains: 2
Atoms: 1,472
Mol. weight: 17.93 kDa
Ligands: MG
Released: 5 Feb 2008

Explore 3BQP in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3BQP contains 12 α-helices and 0 β-strands across 2 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.

Chains A and B: 6 helices, 0 β-strands

Element	Residues	Length
α-helix	5-18	14
α-helix	25-35	11
α-helix	36-38	3
α-helix	41-43	3
α-helix	44-62	19
α-helix	68-74	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Proactivator polypeptide	A, B	protein	80	Homo sapiens	P07602 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>3BQP_1 Proactivator polypeptide (chains A, B)
DGGFCEVCKKLVGYLDRNLEKNSTKQEILAALEKGCSFLPDPYQKQCDQFVAEYEPVLIE
ILVEVMDPSFVCLKIGACPS

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	3

Primary citation

Structures of the human ceramide activator protein saposin D. Popovic, K., Prive, G.G. Acta Crystallogr D Biol Crystallogr (2008) 64:589-594. DOI 10.1107/S0907444908003120 · PubMed

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

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
4V2O 2.13 Å, Structure of saposin B in complex with chloroquine
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

About this viewer

MolViewer shows 3BQP directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.