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Crystal structure of zebrafish asc pyd domain

Analyse Crystal structure of zebrafish asc pyd domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5GPP
Type: protein
Length: 923 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Maltose-binding periplasmic PROTEIN,APOPTOSIS-associated speck-like protein containing a…
UniProt: P0AEY0, Q9I9N6
Ligands: GLC, SO4
Pockets: 16 · best druggability 0.74

Structure

x-ray diffraction · 2 distinct chains · 49% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Maltose-binding periplasmic PROTEIN,APOPTOSIS-associated speck-like protein containing a card	protein	461	49% helix, 16% strand	P0AEY0, Q9I9N6
B	Maltose-binding periplasmic PROTEIN,APOPTOSIS-associated speck-like protein containing a card	protein	462	49% helix, 15% strand	P0AEY0, Q9I9N6

Ligands and binding sites

GLC · alpha-D-glucopyranose · sugar · 4 copies · chains A, B
SO4 · Sulfate ion · ion · 5 copies · chains A, B
ACT · Acetate ion · additive · 6 copies · chains A, B

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

Pockets

16 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	471	0.74	0.83	35	GLC
2	684	0.73	0.79	56	GLC
3	57	0.71	0.97	17	empty
4	60	0.70	0.96	17	empty
5	715	0.69	0.76	54	empty

Interfaces

1 interface between chains.

A–B · 457 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

5GPP · Crystal structure of zebrafish ASC PYD domain · the same entry in another collection · chain A against A, TM-score 1.00
Q9I9N6 · AlphaFold monomer V2.0 prediction for apoptosis-associated speck-like protein containing… · a predicted model of the same protein · chain B against A, TM-score 0.19

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 P0AEY0
Every structure of UniProt Q9I9N6
Elsewhere: RCSB PDB 5GPP · PDBe 5GPP · UniProt P0AEY0 · UniProt Q9I9N6

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