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Activation intermediate 2 of human gastricsin from human stomach

Analyse Activation intermediate 2 of human gastricsin from human stomach in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1AVF
Type: protein
Length: 685 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Gastricsin
EC: 3.4.23.3
UniProt: P20142
Ligands: NA
Pockets: 4 · best druggability 0.73

Structure

x-ray diffraction · 4 distinct chains · 17% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
P	Gastricsin (EC 3.4.23.3)	protein	21	38% helix, 33% strand	P20142
A	Gastricsin (EC 3.4.23.3)	protein	320	14% helix, 45% strand	P20142
Q	Gastricsin (EC 3.4.23.3)	protein	22	32% helix, 32% strand	P20142
J	Gastricsin (EC 3.4.23.3)	protein	322	16% helix, 44% strand	P20142

Ligands and binding sites

NA · Sodium ion · metal · chains A

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

Pockets

4 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	710	0.73	0.79	60	empty
2	373	0.61	0.77	45	empty
3	328	0.58	0.76	39	empty
4	235	0.53	0.77	24	empty

Interfaces

5 interfaces between chains.

Q–J · 1270 Å² buried · 24 hydrogen bonds · protein-protein
P–A · 1230 Å² buried · 24 hydrogen bonds · protein-protein
A–J · 245 Å² buried · 2 hydrogen bonds · protein-protein
P–J · 39 Å² buried · 0 hydrogen bonds · protein-protein
A–Q · 11 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

1AVF · Activation intermediate 2 of human gastricsin from human stomach · the same entry in another collection · chain J against J, TM-score 1.00
P20142 · AlphaFold monomer V2.0 prediction for gastricsin (P20142) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 P20142
Elsewhere: RCSB PDB 1AVF · PDBe 1AVF · UniProt P20142

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