SMTL ID : 7as6.2 (1 other biounit)

2.0 angstrom structure of plant Extended Synaptotagmin 1, C2A domain

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-trimer

Ligands

6 x CD: CADMIUM ION(Non-covalent)

CD.1: 5 residues within 4Å: Chain A: D.24, D.30, D.80, W.81, E.82 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.24, A:D.30, A:D.80, A:W.81, A:E.82 CD.2: 5 residues within 4Å: Chain A: H.51 Chain B: H.51 Chain C: H.51 Ligands: CD.9, CD.16 6 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C, 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: B:H.51, C:H.51, A:H.51, H2O.1, H2O.2, H2O.3 CD.8: 5 residues within 4Å: Chain B: D.24, D.30, D.80, W.81, E.82 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.24, B:D.30, B:D.80, B:W.81, B:E.82 CD.9: 5 residues within 4Å: Chain A: H.51 Chain B: H.51 Chain C: H.51 Ligands: CD.2, CD.16 6 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C, 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: B:H.51, C:H.51, A:H.51, H2O.1, H2O.2, H2O.3 CD.15: 5 residues within 4Å: Chain C: D.24, D.30, D.80, W.81, E.82 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.24, C:D.30, C:D.80, C:W.81, C:E.82 CD.16: 5 residues within 4Å: Chain A: H.51 Chain B: H.51 Chain C: H.51 Ligands: CD.2, CD.9 6 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: A:H.51, C:H.51, B:H.51, H2O.1, H2O.2, H2O.3

6 x NI: NICKEL (II) ION(Non-covalent)

NI.3: 1 residues within 4Å: Chain A: H.105 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.105 NI.4: 2 residues within 4Å: Chain A: H.11, E.61 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.61 NI.10: 1 residues within 4Å: Chain B: H.105 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.105 NI.11: 2 residues within 4Å: Chain B: H.11, E.61 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.61 NI.17: 1 residues within 4Å: Chain C: H.105 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:H.105 NI.18: 2 residues within 4Å: Chain C: H.11, E.61 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:E.61

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

CL.5: 4 residues within 4Å: Chain A: T.48, V.49 Chain C: K.50, H.51 Ligand excluded by PLIP CL.12: 4 residues within 4Å: Chain A: K.50, H.51 Chain B: T.48, V.49 Ligand excluded by PLIP CL.19: 4 residues within 4Å: Chain B: K.50, H.51 Chain C: T.48, V.49 Ligand excluded by PLIP

6 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.6: 6 residues within 4Å: Chain A: K.50, N.53, E.57 Chain B: K.46, T.48 Ligands: EDO.14 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.50, A:N.53, A:E.57 EDO.7: 6 residues within 4Å: Chain A: K.46, T.47, E.60, E.61, F.62 Ligands: EDO.20 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.60, A:E.60 Water bridges: A:E.61 EDO.13: 6 residues within 4Å: Chain B: K.50, N.53, E.57 Chain C: K.46, T.48 Ligands: EDO.21 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.50, B:N.53, B:E.57 EDO.14: 6 residues within 4Å: Chain B: K.46, T.47, E.60, E.61, F.62 Ligands: EDO.6 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.60, B:E.60 Water bridges: B:E.61 EDO.20: 6 residues within 4Å: Chain A: K.46, T.48 Chain C: K.50, N.53, E.57 Ligands: EDO.7 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.50, C:N.53, C:E.57 EDO.21: 6 residues within 4Å: Chain C: K.46, T.47, E.60, E.61, F.62 Ligands: EDO.13 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.60, C:E.60 Water bridges: C:E.61

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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