MolNFT v1 · #123454 · protein

Crystal structure of human juno (crystal form 1)

5JKA · Sperm-egg fusion protein juno: “Crystal structure of human juno (crystal form 1)”. X-ray diffraction, 4 ligands (NAG, BMA, MAN), 4 pockets (best druggability 0.62). MolNFT v1 #123454 on GenesisL1: 3D structure, binding sites and…

PDB: 5JKA
Type: protein
Length: 399 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Sperm-egg fusion protein juno
UniProt: A6ND01
Ligands: NAG, BMA, MAN, CL
Pockets: 4 · best druggability 0.62

Structure

x-ray diffraction · 2 distinct chains · 35% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Sperm-egg fusion protein juno	protein	199	35% helix, 10% strand	A6ND01
A	Sperm-egg fusion protein juno	protein	200	35% helix, 10% strand	A6ND01

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains B
BMA · beta-D-mannopyranose · sugar
MAN · alpha-D-mannopyranose · sugar
CL · Chloride ion · ion · 3 copies · chains B, A

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

Pockets

4 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	244	0.62	0.81	30	empty
2	254	0.61	0.80	32	empty
3	69	0.30	0.73	13	empty
4	71	0.29	0.73	19	empty

Interfaces

1 interface between chains.

B–A · 874 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 disulfide, 1 glycan (disulfide, N-glycosylation).

Compared structures

5JKA · Crystal structure of human JUNO (crystal form 1) · the same entry in another collection · chain B against B, TM-score 1.00
A6ND01 · AlphaFold monomer V2.0 prediction for sperm-egg fusion protein juno (A6ND01) · a predicted model of the same protein · chain B 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 A6ND01
Elsewhere: RCSB PDB 5JKA · PDBe 5JKA · UniProt A6ND01

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