SMTL ID : 2yoa.1 (1 other biounit)

Synaptotagmin-1 C2B domain with phosphoserine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

4 x CA: CALCIUM ION(Non-covalent)

CA.1: 7 residues within 4Å: Chain A: D.34, D.40, D.94, Y.95, D.96 Ligands: CA.2, SEP.4 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:D.34, A:D.40, A:D.94, A:Y.95, SEP.4 CA.2: 6 residues within 4Å: Chain A: M.33, D.34, D.94, D.96, D.102 Ligands: CA.1 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:M.33, A:D.34, A:D.94, A:D.102, H2O.1 CA.3: 3 residues within 4Å: Chain A: D.96, K.100, D.102 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.96, A:K.100, A:D.102, H2O.3, H2O.3, H2O.3 CA.5: 3 residues within 4Å: Chain A: D.40, Y.95 Ligands: SEP.4 No protein-ligand interaction detected (PLIP)

1 x SEP: PHOSPHOSERINE(Non-functional Binders)

SEP.4: 7 residues within 4Å: Chain A: D.34, D.40, Y.95, D.96, K.97 Ligands: CA.1, CA.5 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:D.34, A:K.97 Water bridges: A:N.64, A:N.64, A:N.64, A:K.97, A:K.97, A:I.98 Salt bridges: A:K.97

2 x SCN: THIOCYANATE ION(Non-functional Binders)

SCN.6: 5 residues within 4Å: Chain A: Y.42, K.58, I.61, Y.95, N.101 No protein-ligand interaction detected (PLIP) SCN.7: 4 residues within 4Å: Chain A: T.65, N.67, P.68, Y.69 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Honigmann, A. et al., Phosphatidylinositol 4,5-Bisphosphate Clusters Act as Molecular Beacons for Vesicle Recruitment. Nat.Struct.Mol.Biol. (2013)

Release Date

2013-03-20

Peptides

SYNAPTOTAGMIN-1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

SYNAPTOTAGMIN-1

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