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Crystal structure of human ppca (trigonal crystal form 1)

Analyse Crystal structure of human ppca (trigonal crystal form 1) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4MWS
Type: protein
Length: 826 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lysosomal protective protein
EC: 3.4.16.5
UniProt: P10619
Ligands: NAG, BMA, FUC, MAN
Pockets: 12 · best druggability 0.67

Structure

x-ray diffraction · 1 distinct chain · 35% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Lysosomal protective protein (EC 3.4.16.5)	protein	413	35% helix, 21% strand	P10619

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B
BMA · beta-D-mannopyranose · sugar · 2 copies
FUC · alpha-L-fucopyranose · sugar · 2 copies
MAN · alpha-D-mannopyranose · sugar
GOL · Glycerol · additive · 2 copies · chains A, B

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

Pockets

12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	589	0.67	0.77	63	GOL
2	359	0.61	0.77	39	GOL
3	369	0.58	0.75	35	empty
4	183	0.50	0.77	24	empty
5	51	0.39	0.81	17	empty

Interfaces

1 interface between chains.

A–B · 1814 Å² buried · 19 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide, 4 glycan (disulfide, N-glycosylation).

Compared structures

4MWS · Crystal structure of human PPCA (trigonal crystal form 1) · the same entry in another collection · chain A against A, TM-score 1.00
P10619 · AlphaFold monomer V2.0 prediction for lysosomal protective protein (P10619) · a predicted model of the same protein · chain A against A, TM-score 1.00

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 P10619
Elsewhere: RCSB PDB 4MWS · PDBe 4MWS · UniProt P10619

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