SMTL ID : 8c5h.1

NbSyt1 anti-(rat Synaptotagmin-1) nanobody bound to target cytosolic domain of Synaptotagmin-1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.68 Å

Oligo State

hetero-1-1-mer

Ligands

1 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: D.39, D.45, D.97, F.98 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.39, A:D.45, A:D.97, A:D.97, A:F.98

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 3 residues within 4Å: Chain A: T.68, N.70, P.71 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.68, A:T.68 Water bridges: A:V.72 GOL.3: 4 residues within 4Å: Chain A: F.51, L.53, E.109, K.111 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.109, A:K.111, A:K.111 GOL.4: 7 residues within 4Å: Chain A: L.52, D.55, K.57, F.79, K.80, V.81, K.89 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.55, A:K.57, A:K.80, A:K.89, A:K.89 Water bridges: A:K.58 GOL.5: 7 residues within 4Å: Chain A: F.73, N.74 Chain B: W.54, T.57, T.66, S.107, W.108 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:F.73, B:W.108 GOL.6: 6 residues within 4Å: Chain B: E.69, S.70, V.71, K.72, R.74, K.94 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:V.71 GOL.7: 2 residues within 4Å: Chain B: S.123, S.124 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.123, B:S.124

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Queiroz Zetune Villa Real, K. et al., A Versatile Synaptotagmin-1 Nanobody Provides Perturbation-Free Live Synaptic Imaging And Low Linkage-Error in Super-Resolution Microscopy. Small Methods (2023)

Release Date

2023-08-02

Peptides

Synaptotagmin-1: A
NbSyt1 nanobody: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
S

B
N

Synaptotagmin-1

NbSyt1 nanobody