SMTL ID : 9mym.1

Fertilization IZUMO1 Protein Ectodomain

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.84 Å

Oligo State

monomer

Ligands

2 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG.1: 6 residues within 4Å: Chain A: W.181, N.183, S.185, T.187 Ligands: FUC.2, NAG.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.183, A:S.185 NAG.3: 2 residues within 4Å: Chain A: W.181 Ligands: NAG.1 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.181

1 x FUC: alpha-L-fucopyranose(Non-covalent)

FUC.2: 3 residues within 4Å: Chain A: E.182, N.183 Ligands: NAG.1 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:E.182

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.4: 2 residues within 4Å: Chain A: E.146, R.147 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.146 Water bridges: A:H.148 PEG.6: 4 residues within 4Å: Chain A: N.31, R.34, M.35, H.38 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.31

1 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.5: 3 residues within 4Å: Chain A: I.217, N.218, Q.219 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.218, A:Q.219 Water bridges: A:L.135

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.7: 1 residues within 4Å: Chain A: K.117 Ligand excluded by PLIP

2 x CA: CALCIUM ION(Non-covalent)

CA.8: 1 residues within 4Å: Chain A: N.60 No protein-ligand interaction detected (PLIP) CA.9: 1 residues within 4Å: Chain A: E.84 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.84, A:E.84, H2O.2, H2O.8

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lu, Y. et al., Allosteric inhibition of the IZUMO1-JUNO fertilization complex by the naturally occurring antisperm antibody OBF13. Proc.Natl.Acad.Sci.USA (2025)

Release Date

2025-03-19

Peptides

Izumo sperm-egg fusion protein 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Izumo sperm-egg fusion protein 1