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Myokine structure

Analyse Myokine structure in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4LSD
Type: protein
Length: 761 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fibronectin type III domain-containing protein 5
UniProt: Q8NAU1
Pockets: 8 · best druggability 0.75

Structure

x-ray diffraction · 4 distinct chains · 1% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Fibronectin type III domain-containing protein 5	protein	98	0% helix, 49% strand	Q8NAU1
B, D, E, G, H	Fibronectin type III domain-containing protein 5	protein	94	3% helix, 52% strand	Q8NAU1
C	Fibronectin type III domain-containing protein 5	protein	95	0% helix, 51% strand	Q8NAU1
F	Fibronectin type III domain-containing protein 5	protein	98	0% helix, 48% strand	Q8NAU1

Pockets

8 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	354	0.75	0.86	46	empty
2	455	0.65	0.78	49	empty
3	95	0.41	0.77	22	empty
4	100	0.39	0.76	20	empty
5	184	0.39	0.72	28	empty

Interfaces

9 interfaces between chains.

C–D · 725 Å² buried · 14 hydrogen bonds · protein-protein
G–H · 713 Å² buried · 15 hydrogen bonds · protein-protein
E–F · 707 Å² buried · 17 hydrogen bonds · protein-protein
A–B · 675 Å² buried · 12 hydrogen bonds · protein-protein
A–F · 506 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 modified (engineered).

Compared structures

4LSD · Myokine structure · the same entry in another collection · chain H against H, TM-score 1.00
Q8NAU1 · AlphaFold monomer V2.0 prediction for fibronectin type III domain- containing protein 5… · a predicted model of the same protein · chain H against A, TM-score 0.97

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 Q8NAU1
Elsewhere: RCSB PDB 4LSD · PDBe 4LSD · UniProt Q8NAU1

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