SMTL ID : 7atp.2 (1 other biounit)

2.0 angstrom structure in complex with Ca of plant Extended Synaptotagmin 1, C2A domain

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-trimer

Ligands

6 x CA: CALCIUM ION(Non-covalent)

CA.1: 6 residues within 4Å: Chain A: D.24, D.30, D.80, W.81, E.82 Ligands: CA.2 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.24, A:D.30, A:D.80, A:W.81, H2O.1 CA.2: 6 residues within 4Å: Chain A: K.23, D.24, D.80, E.82, E.88 Ligands: CA.1 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.24, A:D.80, A:E.82, A:E.88, H2O.1 CA.5: 6 residues within 4Å: Chain B: D.24, D.30, D.80, W.81, E.82 Ligands: CA.6 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.24, B:D.30, B:D.80, B:W.81, H2O.1 CA.6: 6 residues within 4Å: Chain B: K.23, D.24, D.80, E.82, E.88 Ligands: CA.5 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.24, B:D.80, B:E.82, B:E.88, H2O.1 CA.9: 6 residues within 4Å: Chain C: D.24, D.30, D.80, W.81, E.82 Ligands: CA.10 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.24, C:D.30, C:D.80, C:W.81, H2O.1 CA.10: 6 residues within 4Å: Chain C: K.23, D.24, D.80, E.82, E.88 Ligands: CA.9 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.24, C:D.80, C:E.82, C:E.88, H2O.2

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 11 residues within 4Å: Chain A: V.49, H.51 Chain B: V.49, H.51 Chain C: V.49, H.51 Ligands: ZN.4, CL.7, ZN.8, CL.11, ZN.12 Ligand excluded by PLIP CL.7: 11 residues within 4Å: Chain A: V.49, H.51 Chain B: V.49, H.51 Chain C: V.49, H.51 Ligands: CL.3, ZN.4, ZN.8, CL.11, ZN.12 Ligand excluded by PLIP CL.11: 11 residues within 4Å: Chain A: V.49, H.51 Chain B: V.49, H.51 Chain C: V.49, H.51 Ligands: CL.3, ZN.4, CL.7, ZN.8, ZN.12 Ligand excluded by PLIP

3 x ZN: ZINC ION(Non-covalent)

ZN.4: 8 residues within 4Å: Chain A: H.51 Chain B: H.51 Chain C: H.51 Ligands: CL.3, CL.7, ZN.8, CL.11, ZN.12 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 1 interactions with chain C Metal complexes: B:H.51, A:H.51, C:H.51 ZN.8: 8 residues within 4Å: Chain A: H.51 Chain B: H.51 Chain C: H.51 Ligands: CL.3, ZN.4, CL.7, CL.11, ZN.12 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 1 interactions with chain C Metal complexes: B:H.51, A:H.51, C:H.51 ZN.12: 8 residues within 4Å: Chain A: H.51 Chain B: H.51 Chain C: H.51 Ligands: CL.3, ZN.4, CL.7, ZN.8, CL.11 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 1 interactions with chain C Metal complexes: B:H.51, A:H.51, C:H.51

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Benavente, J.L. et al., The structure and flexibility analysis of the Arabidopsis synaptotagmin 1 reveal the basis of its regulation at membrane contact sites. Life Sci Alliance (2021)

Release Date

2021-08-18

Peptides

Synaptotagmin-1: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Synaptotagmin-1

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