SMTL ID : 5ccj.5 (4 other biounits)

Crystal structure of the quintuple mutant of the synaptotagmin-1 C2B domain

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-tetramer

Ligands

27 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 3 residues within 4Å: Chain A: T.114, G.115 Chain B: K.151 Ligand excluded by PLIP GOL.2: 7 residues within 4Å: Chain A: Y.42, K.58, T.59, T.60, I.61, N.101 Ligands: SO4.8 Ligand excluded by PLIP GOL.3: 3 residues within 4Å: Chain A: T.65, L.66, N.67 Ligand excluded by PLIP GOL.4: 6 residues within 4Å: Chain A: V.107, F.108, S.113, T.114, E.117, M.147 Ligand excluded by PLIP GOL.5: 5 residues within 4Å: Chain A: R.53, L.54, K.55, K.56 Ligands: SO4.7 Ligand excluded by PLIP GOL.6: 6 residues within 4Å: Chain A: A.130, P.131 Chain B: R.119, S.122, D.123 Ligands: SO4.21 Ligand excluded by PLIP GOL.12: 2 residues within 4Å: Chain B: K.57, F.74 Ligand excluded by PLIP GOL.13: 6 residues within 4Å: Chain B: K.58, T.59, T.60, I.61, Y.95 Ligands: SO4.23 Ligand excluded by PLIP GOL.14: 5 residues within 4Å: Chain B: V.23, N.71, S.73 Chain C: A.126 Ligands: GOL.40 Ligand excluded by PLIP GOL.15: 5 residues within 4Å: Chain B: K.55, K.57, S.75, F.76, E.77 Ligand excluded by PLIP GOL.16: 2 residues within 4Å: Chain B: T.60, I.61 Ligand excluded by PLIP GOL.17: 5 residues within 4Å: Chain B: A.116, R.119, T.137 Ligands: SO4.21, SO4.24 Ligand excluded by PLIP GOL.18: 4 residues within 4Å: Chain B: W.69, N.71 Chain C: P.128, A.129 Ligand excluded by PLIP GOL.27: 6 residues within 4Å: Chain C: V.107, F.108, S.113, T.114, E.117, Q.139 Ligand excluded by PLIP GOL.28: 3 residues within 4Å: Chain C: T.65, L.66, N.67 Ligand excluded by PLIP GOL.29: 3 residues within 4Å: Chain C: K.62, K.63, T.65 Ligand excluded by PLIP GOL.30: 9 residues within 4Å: Chain A: L.25, W.69, N.71 Chain B: A.126, N.127 Chain C: T.114, G.115 Chain D: K.151 Ligands: SO4.9 Ligand excluded by PLIP GOL.31: 4 residues within 4Å: Chain C: R.53, L.54, K.55, K.56 Ligand excluded by PLIP GOL.32: 5 residues within 4Å: Chain C: Y.42, K.44, L.93, N.101 Ligands: SO4.34 Ligand excluded by PLIP GOL.36: 7 residues within 4Å: Chain D: Y.42, K.58, T.59, I.61, Y.95, N.101 Ligands: SO4.46 Ligand excluded by PLIP GOL.37: 2 residues within 4Å: Ligands: GOL.39, GOL.43 Ligand excluded by PLIP GOL.38: 5 residues within 4Å: Chain B: A.17, K.19 Chain D: E.143, A.146, M.147 Ligand excluded by PLIP GOL.39: 5 residues within 4Å: Chain D: V.23, N.71, E.72, S.73 Ligands: GOL.37 Ligand excluded by PLIP GOL.40: 3 residues within 4Å: Chain D: T.114, G.115 Ligands: GOL.14 Ligand excluded by PLIP GOL.41: 2 residues within 4Å: Chain D: W.69, N.71 Ligand excluded by PLIP GOL.42: 1 residues within 4Å: Chain D: D.123 Ligand excluded by PLIP GOL.43: 2 residues within 4Å: Chain D: P.131 Ligands: GOL.37 Ligand excluded by PLIP

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

SO4.7: 6 residues within 4Å: Chain A: K.44, H.46, R.53, K.56 Ligands: GOL.5, SO4.8 Ligand excluded by PLIP SO4.8: 6 residues within 4Å: Chain A: Y.42, K.44, K.56, N.101 Ligands: GOL.2, SO4.7 Ligand excluded by PLIP SO4.9: 6 residues within 4Å: Chain A: W.69, N.71 Chain D: K.85, Y.111, K.151 Ligands: GOL.30 Ligand excluded by PLIP SO4.10: 2 residues within 4Å: Chain A: K.52, R.53 Ligand excluded by PLIP SO4.11: 1 residues within 4Å: Chain A: K.31 Ligand excluded by PLIP SO4.19: 5 residues within 4Å: Chain B: K.44, H.46, R.53, K.56 Ligands: SO4.23 Ligand excluded by PLIP SO4.20: 3 residues within 4Å: Chain B: K.52, R.53, K.152 Ligand excluded by PLIP SO4.21: 5 residues within 4Å: Chain B: R.119, Q.134 Chain C: Y.111 Ligands: GOL.6, GOL.17 Ligand excluded by PLIP SO4.22: 3 residues within 4Å: Chain B: T.65, L.66, N.67 Ligand excluded by PLIP SO4.23: 6 residues within 4Å: Chain B: Y.42, K.44, K.56, K.58 Ligands: GOL.13, SO4.19 Ligand excluded by PLIP SO4.24: 4 residues within 4Å: Chain B: G.115, A.116, R.119 Ligands: GOL.17 Ligand excluded by PLIP SO4.25: 3 residues within 4Å: Chain B: I.98, G.99, K.100 Ligand excluded by PLIP SO4.26: 2 residues within 4Å: Chain B: K.62, K.63 Ligand excluded by PLIP SO4.33: 2 residues within 4Å: Chain C: W.69, N.71 Ligand excluded by PLIP SO4.34: 3 residues within 4Å: Chain C: K.44, H.46 Ligands: GOL.32 Ligand excluded by PLIP SO4.35: 2 residues within 4Å: Chain C: K.52, R.53 Ligand excluded by PLIP SO4.44: 3 residues within 4Å: Chain D: A.116, R.119, Q.134 Ligand excluded by PLIP SO4.45: 5 residues within 4Å: Chain D: K.44, H.46, R.53, K.56 Ligands: SO4.46 Ligand excluded by PLIP SO4.46: 7 residues within 4Å: Chain D: Y.42, K.44, K.56, K.58, N.101 Ligands: GOL.36, SO4.45 Ligand excluded by PLIP SO4.47: 3 residues within 4Å: Chain D: T.65, L.66, N.67 Ligand excluded by PLIP SO4.48: 3 residues within 4Å: Chain D: K.52, R.53, K.152 Ligand excluded by PLIP SO4.49: 3 residues within 4Å: Chain D: G.115, A.116, R.119 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhou, Q. et al., Architecture of the synaptotagmin-SNARE machinery for neuronal exocytosis. Nature (2015)

Release Date

2015-08-12

Peptides

Synaptotagmin-1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Synaptotagmin-1

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