SMTL ID : 6gf7.1

Molecular basis of egg coat filament cross-linking: Zn-SAD structure of the partially deglycosylated ZP1 ZP-N1 domain homodimer

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-dimer

Ligands

2 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.1: 4 residues within 4Å: Chain A: N.47, W.54, L.55, N.56 No protein-ligand interaction detected (PLIP) NAG.7: 1 residues within 4Å: Chain B: N.47 No protein-ligand interaction detected (PLIP)

9 x ZN: ZINC ION(Non-covalent)(Non-functional Binders)

ZN.2: 3 residues within 4Å: Chain A: C.51, H.53, H.73 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.53, A:H.73, H2O.1 ZN.3: 3 residues within 4Å: Chain A: H.11, D.13, L.22 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.11, A:D.13, A:D.13, H2O.1, H2O.1 ZN.4: 2 residues within 4Å: Chain A: H.32, E.44 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.32, A:E.44, A:E.44, H2O.1, H2O.1 ZN.5: 2 residues within 4Å: Chain A: K.34, E.88 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.88, A:E.88, H2O.1 ZN.6: 1 residues within 4Å: Chain A: D.16 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.16, H2O.1, H2O.1, H2O.1 ZN.8: 4 residues within 4Å: Chain B: C.51, H.53, C.72, H.73 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.53 ZN.9: 3 residues within 4Å: Chain B: H.11, D.13 Ligands: ZN.10 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.11, B:D.13, B:D.13, H2O.1 ZN.10: 1 residues within 4Å: Ligands: ZN.9 No protein-ligand interaction detected (PLIP) ZN.11: 2 residues within 4Å: Chain B: H.32, E.88 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.32, B:E.88, H2O.1

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
B

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

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