SMTL ID : 4wee.1

High-resolution structure of Synaptotagmin 1 C2A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 0.89 Å

Oligo State

monomer

Ligands

7 x NA: SODIUM ION(Non-functional Binders)

NA.1: 5 residues within 4Å: Chain A: L.13, D.14, M.16, E.18 Ligands: NA.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:M.16, A:M.16 NA.2: 5 residues within 4Å: Chain A: Q.42, A.43, A.44, N.81, W.137 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.81 NA.3: 4 residues within 4Å: Chain A: D.14, E.18 Ligands: NA.1, NA.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.14, A:E.18 NA.4: 2 residues within 4Å: Chain A: D.14 Ligands: NA.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.14 NA.5: 7 residues within 4Å: Chain A: V.17, E.18, L.20, L.140, Q.141, S.142 Ligands: NA.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.18, A:L.140, A:S.142 NA.6: 9 residues within 4Å: Chain A: V.17, E.18, K.19, L.20, G.21, D.139, L.140 Ligands: NA.5, NA.7 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.20, A:G.21, A:L.140 Water bridges: A:K.22 NA.7: 7 residues within 4Å: Chain A: V.17, E.18, K.19, L.20, K.22, D.139 Ligands: NA.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.22, A:D.139, A:D.139

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.8: 3 residues within 4Å: Chain A: R.77, F.109, R.111 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.111 Salt bridges: A:R.77, A:R.111 SO4.9: 4 residues within 4Å: Chain A: G.52, G.53, T.54, K.78 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.54, A:T.54 Salt bridges: A:K.78

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dominguez, M.J. et al., The AD3 locus of synaptotagmin-1 C2 domains modulates domain stability. Biophys.J. (2024)

Release Date

2014-10-01

Peptides

Synaptotagmin-1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Synaptotagmin-1