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Crystal structure of mouse interleukin-34

Analyse Crystal structure of mouse interleukin-34 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4EXN
Type: protein
Length: 677 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Interleukin-34
UniProt: Q8R1R4
Ligands: NAG, BMA, MAN
Pockets: 3 · best druggability 0.54

Structure

x-ray diffraction · 3 distinct chains · 57% helix, 4% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, F	Interleukin-34	protein	172	58% helix, 3% strand	Q8R1R4
B	Interleukin-34	protein	162	57% helix, 4% strand	Q8R1R4
E	Interleukin-34	protein	171	56% helix, 4% strand	Q8R1R4

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 16 copies · chains A, B, E, F
BMA · beta-D-mannopyranose · sugar · 13 copies · chains A, B, F, E
MAN · alpha-D-mannopyranose · sugar · 3 copies · chains E

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

Pockets

3 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	289	0.54	0.75	51	empty
2	55	0.32	0.76	13	empty
3	52	0.30	0.76	11	empty

Interfaces

4 interfaces between chains.

A–B · 639 Å² buried · 4 hydrogen bonds · protein-protein
E–F · 631 Å² buried · 3 hydrogen bonds · protein-protein
B–F · 195 Å² buried · 0 hydrogen bonds · protein-protein
B–E · 31 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide, 8 glycan (disulfide, N-glycosylation).

Compared structures

4EXN · Crystal structure of mouse Interleukin-34 · the same entry in another collection · chain A against A, TM-score 1.00
Q8R1R4 · AlphaFold monomer V2.0 prediction for interleukin-34 (Q8R1R4) · 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 Q8R1R4
Elsewhere: RCSB PDB 4EXN · PDBe 4EXN · UniProt Q8R1R4

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