MolNFT v1 · #108295 · protein

Structure of saposin B in complex with chloroquine

4V2O · Saposin-B: “Structure of saposin B in complex with chloroquine”. X-ray diffraction, 1 ligand (CLQ), 3 pockets (best druggability 0.74). MolNFT v1 #108295 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4V2O
Type: protein
Length: 240 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Saposin-B
UniProt: P07602
Ligands: CLQ
Pockets: 3 · best druggability 0.74

Structure

x-ray diffraction · 2 distinct chains · 82% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Saposin-B	protein	78	82% helix, 0% strand	P07602
B, C	Saposin-B	protein	81	81% helix, 0% strand	P07602

Ligands and binding sites

CLQ · N4-(7-chloro-quinolin-4-yl)-N1,N1-diethyl-pentane-1,4-diamine · ligand · 2 copies · chains B, A, C

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	880	0.74	0.77	50	empty
2	137	0.41	0.75	20	empty
3	143	0.41	0.73	19	empty

Interfaces

2 interfaces between chains.

A–C · 931 Å² buried · 11 hydrogen bonds · protein-protein
B–C · 66 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 9 disulfide (disulfide).

Compared structures

4V2O · Structure of saposin B in complex with chloroquine · 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 B against A, TM-score 0.92

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 4V2O · PDBe 4V2O · UniProt P07602

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