SMTL ID : 6gf8.1 (1 other biounit)

Molecular basis of egg coat filament cross-linking: structure of the glycosylated ZP1 ZP-N1 domain homodimer

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

homo-dimer

Ligands

2 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUC.1: 5 residues within 4Å: Chain A: N.47, W.54, L.55, N.56 Ligands: MPD.2 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.4: 5 residues within 4Å: Chain B: N.47, W.54, L.55, N.56 Ligands: MPD.5 No protein-ligand interaction detected (PLIP)

4 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.2: 4 residues within 4Å: Chain A: F.17, G.18, W.54 Ligands: NAG-NAG-FUC.1 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.17 MPD.3: 6 residues within 4Å: Chain A: F.43, H.73 Chain B: I.50, E.70, G.71, C.72 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:I.50, A:F.43 Hydrogen bonds: B:E.70 MPD.5: 4 residues within 4Å: Chain B: F.17, G.18, W.54 Ligands: NAG-NAG-FUC.4 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.17 MPD.6: 6 residues within 4Å: Chain A: I.50, E.70, G.71, C.72 Chain B: F.43, H.73 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:I.50, B:F.43 Hydrogen bonds: A:E.70

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nishimura, K. et al., Molecular basis of egg coat cross-linking sheds light on ZP1-associated female infertility. Nat Commun (2019)

Release Date

2019-06-19

Peptides

Zona pellucida sperm-binding protein 1,Zona pellucida sperm-binding protein 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Zona pellucida sperm-binding protein 1,Zona pellucida sperm-binding protein 1

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