Research workbench

Murine saposin-D (sapd), open conformation

Analyse Murine saposin-D (sapd), open conformation in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5U85
Type: protein
Length: 155 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Saposin-D
UniProt: Q61207
Pockets: 1 · best druggability 0.81

Structure

x-ray diffraction · 2 distinct chains · 79% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Saposin-D	protein	78	77% helix, 0% strand	Q61207
B	Saposin-D	protein	77	81% helix, 0% strand	Q61207

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	566	0.81	0.86	43	empty

Interfaces

1 interface between chains.

A–B · 1517 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

5U85 · Murine saposin-D (SapD), open conformation · the same entry in another collection · chain A against A, TM-score 1.00
Q61207 · AlphaFold monomer V2.0 prediction for prosaposin (Q61207) · a predicted model of the same protein · chain A against A, TM-score 0.60

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 Q61207
Elsewhere: RCSB PDB 5U85 · PDBe 5U85 · UniProt Q61207

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