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Crystal structure of the beta subunit of luteinizing hormone

Analyse Crystal structure of the beta subunit of luteinizing hormone in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6P57
Type: protein
Length: 224 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lutropin subunit beta
UniProt: P04651
Ligands: NAG, BMA, FUL, MAN
Pockets: 2 · best druggability 0.78

Structure

x-ray diffraction · 2 distinct chains · 0% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Lutropin subunit beta	protein	106	0% helix, 40% strand	P04651
B	Lutropin subunit beta	protein	118	0% helix, 31% strand	P04651

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, B
BMA · beta-D-mannopyranose · sugar · 2 copies
FUL · beta-L-fucopyranose · sugar · 2 copies · chains A, B
MAN · alpha-D-mannopyranose · sugar · 2 copies
BOG · octyl beta-D-glucopyranoside · additive · 2 copies · chains 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, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	829	0.78	0.81	82	empty
2	419	0.57	0.74	41	empty

Interfaces

1 interface between chains.

A–B · 911 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

6P57 · Crystal Structure of the Beta Subunit of Luteinizing Hormone · the same entry in another collection · chain A against A, TM-score 1.00
P04651 · AlphaFold monomer V2.0 prediction for lutropin subunit beta (P04651) · a predicted model of the same protein · chain A against A, TM-score 0.73

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 P04651
Elsewhere: RCSB PDB 6P57 · PDBe 6P57 · UniProt P04651

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