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Crystal structure of asc pyd domain and rb-B7

Analyse Crystal structure of asc pyd domain and rb-B7 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7E5B
Type: protein
Length: 712 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Repebody (rb-B7); Apoptosis-associated speck-like protein containing a card
UniProt: Q9ULZ3
Pockets: 6 · best druggability 0.60

Structure

x-ray diffraction · 4 distinct chains · 30% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Repebody (rb-B7)	protein	265	17% helix, 13% strand	—
B	Repebody (rb-B7)	protein	266	17% helix, 13% strand	—
C	Apoptosis-associated speck-like protein containing a card	protein	91	69% helix, 0% strand	Q9ULZ3
D	Apoptosis-associated speck-like protein containing a card	protein	90	68% helix, 0% strand	Q9ULZ3

Ligands and binding sites

GOL · Glycerol · additive · 2 copies · chains A, D, B, C

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

Pockets

6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	223	0.60	0.80	29	GOL
2	235	0.60	0.80	30	GOL
3	88	0.38	0.76	25	empty
4	90	0.36	0.75	24	empty
5	124	0.34	0.72	30	empty

Interfaces

3 interfaces between chains.

B–C · 973 Å² buried · 21 hydrogen bonds · protein-protein
A–D · 930 Å² buried · 21 hydrogen bonds · protein-protein
A–B · 666 Å² buried · 21 hydrogen bonds · protein-protein

Compared structures

7E5B · Crystal structure of ASC PYD Domain and Rb-B7 · the same entry in another collection · chain A against A, TM-score 1.00
Q9ULZ3 · AlphaFold monomer V2.0 prediction for apoptosis-associated speck-like protein containing… · a predicted model of the same protein · chain D against A, TM-score 0.94

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 Q9ULZ3
Elsewhere: RCSB PDB 7E5B · PDBe 7E5B · UniProt Q9ULZ3

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