MolNFT v1 · #50193 · protein

Crystal structure of human saposin D

2RB3 · Proactivator polypeptide: “Crystal structure of human saposin D”. X-ray diffraction, 1 ligand (SO4), 2 pockets (best druggability 0.52). MolNFT v1 #50193 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2RB3
Type: protein
Length: 315 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Proactivator polypeptide
UniProt: P07602
Ligands: SO4
Pockets: 2 · best druggability 0.52

Structure

x-ray diffraction · 2 distinct chains · 73% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Proactivator polypeptide	protein	79	72% helix, 0% strand	P07602
D	Proactivator polypeptide	protein	78	74% helix, 0% strand	P07602

Ligands and binding sites

SO4 · Sulfate ion · ion · 3 copies · chains A, B, C
GOL · Glycerol · additive · 2 copies · chains B, D

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

Pockets

2 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	175	0.52	0.78	25	empty
2	72	0.29	0.73	15	empty

Interfaces

4 interfaces between chains.

B–C · 564 Å² buried · 6 hydrogen bonds · protein-protein
A–D · 517 Å² buried · 4 hydrogen bonds · protein-protein
A–B · 417 Å² buried · 5 hydrogen bonds · protein-protein
B–D · 15 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide (disulfide).

Compared structures

2RB3 · Crystal Structure of Human Saposin D · 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 0.57

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 2RB3 · PDBe 2RB3 · UniProt P07602

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