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Crystal structure of the mouse KIRREL3 D1 homodimer

Analyse Crystal structure of the mouse KIRREL3 D1 homodimer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7LU6
Type: protein
Length: 804 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Kin of irre-like protein 3
UniProt: Q8BR86
Ligands: NA
Pockets: 7 · best druggability 0.54

Structure

x-ray diffraction · 4 distinct chains · 6% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Kin of irre-like protein 3	protein	102	6% helix, 41% strand	Q8BR86
B	Kin of irre-like protein 3	protein	101	6% helix, 42% strand	Q8BR86
D, E, F, G	Kin of irre-like protein 3	protein	100	6% helix, 42% strand	Q8BR86
H	Kin of irre-like protein 3	protein	99	6% helix, 40% strand	Q8BR86

Ligands and binding sites

NA · Sodium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H

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

Pockets

7 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	68	0.54	0.87	22	empty
2	65	0.41	0.80	20	empty
3	68	0.41	0.80	16	empty
4	53	0.40	0.81	17	empty
5	55	0.36	0.79	16	empty

Interfaces

7 interfaces between chains.

F–G · 745 Å² buried · 15 hydrogen bonds · protein-protein
C–D · 722 Å² buried · 6 hydrogen bonds · protein-protein
B–E · 701 Å² buried · 13 hydrogen bonds · protein-protein
A–B · 699 Å² buried · 6 hydrogen bonds · protein-protein
G–H · 670 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

7LU6 · Crystal structure of the mouse Kirrel3 D1 homodimer · the same entry in another collection · chain H against H, TM-score 1.00
Q8BR86 · AlphaFold monomer V2.0 prediction for kin of irre-like protein 3 (Q8BR86) · 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 Q8BR86
Elsewhere: RCSB PDB 7LU6 · PDBe 7LU6 · UniProt Q8BR86

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