9AXG: Saposin-B

Human saposin B in the presence of globotriaosylceramide-NBD. Determined by X-ray diffraction at 2.68 Å resolution. Released 13 Mar 2024.

Method: X-ray diffraction
Resolution: 2.68 Å
Organism: Homo sapiens
Chains: 2
Atoms: 1,166
Mol. weight: 18.3 kDa
Ligands: MLI
Released: 13 Mar 2024

Explore 9AXG in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9AXG contains 10 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.

Chain A: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	2-20	19
α-helix	24-34	11
α-helix	35-38	4
α-helix	43-63	21
α-helix	67-74	8

Chain B: 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	41-63	23
α-helix	67-74	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Saposin-B	A, B	protein	82	Homo sapiens	P07602 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>9AXG_1 Saposin-B (chains A, B)
GASGDVCQDCIQMVTDIQTAVRTNSTFVQALVEHVKEECDRLGPGMADICKNYISQYSEI
AIQMMMHMQPKEICALVGFCDE

Ligands and cofactors

ID	Name	Formula	Copies
MLI	Malonate ion	C3 H2 O4	1

Primary citation

Human Saposin B Ligand Binding and Presentation to alpha-Galactosidase A. Sawyer, T.K., Aral, E., Staros, J.V. et al. bioRxiv (2024). DOI 10.1101/2024.04.04.584535 · 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
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

Browse structure collections

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