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Crystal structure of human saposin B

Analyse Crystal structure of human saposin B in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1N69
Type: protein
Length: 236 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Saposin B
UniProt: P07602
Ligands: 3PE
Pockets: 3 · best druggability 0.85

Structure

x-ray diffraction · 2 distinct chains · 77% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Saposin B	protein	78	79% helix, 0% strand	P07602
B	Saposin B	protein	80	75% helix, 0% strand	P07602

Ligands and binding sites

3PE · 1,2-diacyl-sn-glycero-3-phosphoethanolamine · ligand · chains A, B

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

Pockets

3 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	1163	0.85	0.86	60	3PE
2	175	0.45	0.75	26	empty
3	85	0.34	0.74	23	empty

Interfaces

3 interfaces between chains.

A–B · 1338 Å² buried · 13 hydrogen bonds · protein-protein
B–C · 447 Å² buried · 6 hydrogen bonds · protein-protein
A–C · 105 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 9 disulfide (disulfide).

Compared structures

1N69 · Crystal structure of human saposin B · 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 A against A, TM-score 0.82

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 1N69 · PDBe 1N69 · UniProt P07602

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