MolNFT v1 · #123455 · protein

Crystal structure of human juno (crystal form 2)

5JKB · Sperm-egg fusion protein juno: “Crystal structure of human juno (crystal form 2)”. X-ray diffraction, 1 ligand (CL), 7 pockets (best druggability 0.70). MolNFT v1 #123455 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5JKB
Type: protein
Length: 792 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Sperm-egg fusion protein juno
UniProt: A6ND01
Ligands: CL
Pockets: 7 · best druggability 0.70

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Sperm-egg fusion protein juno	protein	199	35% helix, 10% strand	A6ND01
C, D	Sperm-egg fusion protein juno	protein	197	35% helix, 11% strand	A6ND01

Ligands and binding sites

CL · Chloride ion · ion · 4 copies · chains A, B, C, D

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

Pockets

7 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	955	0.70	0.75	72	empty
2	395	0.67	0.80	39	empty
3	411	0.65	0.78	36	empty
4	269	0.62	0.80	33	empty
5	324	0.62	0.79	37	empty

Interfaces

4 interfaces between chains.

B–C · 849 Å² buried · 7 hydrogen bonds · protein-protein
C–D · 618 Å² buried · 14 hydrogen bonds · protein-protein
A–C · 393 Å² buried · 9 hydrogen bonds · protein-protein
A–B · 67 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 32 disulfide (disulfide).

Compared structures

5JKB · Crystal structure of human JUNO (crystal form 2) · the same entry in another collection · chain A against A, 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 C 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 5JKB · PDBe 5JKB · UniProt A6ND01

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