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Crystal structure of ankb LIR/LC3B complex

Analyse Crystal structure of ankb LIR/LC3B complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5YIS
Type: protein
Length: 274 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Microtubule-associated proteins 1A/1B light chain 3B; Ankyrin-2
UniProt: Q9CQV6, Q01484
Ligands: PO4
Pockets: 2 · best druggability 0.66

Structure

x-ray diffraction · 4 distinct chains · 35% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Microtubule-associated proteins 1A/1B light chain 3B	protein	113	33% helix, 21% strand	Q9CQV6
B	Microtubule-associated proteins 1A/1B light chain 3B	protein	122	37% helix, 22% strand	Q9CQV6
D	Ankyrin-2	protein	13	38% helix, 23% strand	Q01484
C	Ankyrin-2	protein	26	31% helix, 15% strand	Q01484

Ligands and binding sites

PO4 · Phosphate ion · ion · chains B
GOL · Glycerol · additive · 2 copies · chains A, B

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

Pockets

2 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	191	0.66	0.85	33	empty
2	107	0.38	0.75	26	GOL

Interfaces

4 interfaces between chains.

A–C · 942 Å² buried · 16 hydrogen bonds · protein-protein
B–C · 800 Å² buried · 10 hydrogen bonds · protein-protein
B–D · 622 Å² buried · 5 hydrogen bonds · protein-protein
A–B · 291 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

5YIS · Crystal Structure of AnkB LIR/LC3B complex · the same entry in another collection · chain A against A, TM-score 1.00
Q9CQV6 · AlphaFold monomer V2.0 prediction for microtubule-associated proteins 1A/1B light chain… · a predicted model of the same protein · chain B against A, TM-score 0.98

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 Q9CQV6
Every structure of UniProt Q01484
Elsewhere: RCSB PDB 5YIS · PDBe 5YIS · UniProt Q9CQV6 · UniProt Q01484

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