SMTL ID : 6u4u.1

1.3 A structure of a pathogenic human Syt 1 C2B (I368T)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

monomer

Ligands

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

SO4.1: 5 residues within 4Å: Chain A: Y.47, K.49, K.61, L.98, N.106 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:Y.47, A:Y.47, A:N.106 Water bridges: A:N.106, A:N.106, A:N.106 Salt bridges: A:K.49, A:K.61 SO4.2: 4 residues within 4Å: Chain A: A.121, E.122, H.141, T.142 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:T.142, A:T.142, A:T.142 Water bridges: A:A.121, A:A.121, A:W.140, A:H.141 Salt bridges: A:H.141 SO4.3: 4 residues within 4Å: Chain A: K.49, H.51, R.58, K.61 4 PLIP interactions: 4 interactions with chain A Salt bridges: A:K.49, A:H.51, A:R.58, A:K.61 SO4.4: 4 residues within 4Å: Chain A: N.69, T.70, L.71, N.72 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.70, A:T.70, A:L.71, A:N.72, A:N.72 SO4.5: 2 residues within 4Å: Chain A: Q.139, W.140 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.140 Water bridges: A:A.138, A:W.140, A:W.140 SO4.6: 2 residues within 4Å: Chain A: E.7, K.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.8 Water bridges: A:E.7 Salt bridges: A:K.8 SO4.7: 3 residues within 4Å: Chain A: G.120, A.121, R.124 3 PLIP interactions: 3 interactions with chain A Water bridges: A:A.121, A:A.121 Salt bridges: A:R.124 SO4.8: 2 residues within 4Å: Chain A: K.57, R.58 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.58 Salt bridges: A:R.58 SO4.9: 3 residues within 4Å: Chain A: E.86, Q.87, K.90 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.86, A:Q.87, A:Q.87 Water bridges: A:K.90 Salt bridges: A:K.90

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bradberry, M.M. et al., Molecular Basis for Synaptotagmin-1-Associated Neurodevelopmental Disorder. Neuron (2020)

Release Date

2020-05-13

Peptides

Synaptotagmin-1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Synaptotagmin-1