SMTL ID : 3sg5.1

Crystal Structure of Dimeric GCaMP3-D380Y, QP(linker 1), LP(linker 2)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

8 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: D.429, D.431, D.433, Q.435, E.440 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.429, A:D.431, A:D.433, A:Q.435, H2O.1 CA.2: 5 residues within 4Å: Chain A: D.320, D.322, D.324, T.326, E.331 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.320, A:D.322, A:D.324, A:E.331, H2O.2 CA.3: 5 residues within 4Å: Chain A: D.393, D.395, N.397, Y.399, E.404 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.393, A:Y.399, A:E.404, A:E.404, H2O.1 CA.4: 5 residues within 4Å: Chain A: D.356, D.358, D.360, T.362, E.367 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.356, A:D.358, A:D.360, A:T.362, H2O.2 CA.10: 5 residues within 4Å: Chain B: D.429, D.431, D.433, Q.435, E.440 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.429, B:D.431, B:D.433, B:Q.435, H2O.5 CA.11: 5 residues within 4Å: Chain B: D.320, D.322, D.324, T.326, E.331 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.320, B:D.322, B:D.324, B:E.331, H2O.6 CA.12: 5 residues within 4Å: Chain B: D.393, D.395, N.397, Y.399, E.404 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.393, B:Y.399, B:E.404, B:E.404, H2O.5 CA.13: 5 residues within 4Å: Chain B: D.356, D.358, D.360, T.362, E.367 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.356, B:D.358, B:D.360, B:T.362, H2O.6

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

SO4.5: 6 residues within 4Å: Chain A: P.213, W.214, P.215, H.294, L.296, Y.298 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.214, A:L.296 Salt bridges: A:H.294 SO4.6: 4 residues within 4Å: Chain A: K.118, S.120, T.305, E.306 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.120, A:E.306 Salt bridges: A:K.118 SO4.7: 4 residues within 4Å: Chain A: A.403, R.406, H.407 Ligands: SO4.8 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.406, A:H.407 SO4.8: 4 residues within 4Å: Chain A: A.403, R.406 Ligands: SO4.7, GOL.9 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.406 SO4.14: 6 residues within 4Å: Chain B: P.213, W.214, P.215, H.294, L.296, Y.298 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:W.214, B:L.296 Salt bridges: B:H.294 SO4.15: 4 residues within 4Å: Chain B: K.118, S.120, T.305, E.306 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.120, B:E.306 Salt bridges: B:K.118 SO4.16: 4 residues within 4Å: Chain B: A.403, R.406, H.407 Ligands: SO4.17 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.406, B:H.407 SO4.17: 4 residues within 4Å: Chain B: A.403, R.406 Ligands: SO4.16, GOL.18 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.406

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 4 residues within 4Å: Chain A: A.402, R.406, D.422 Ligands: SO4.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.406, A:R.406 Water bridges: A:D.422 GOL.18: 4 residues within 4Å: Chain B: A.402, R.406, D.422 Ligands: SO4.17 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.406, B:R.406 Water bridges: B:D.422

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Akerboom, J. et al., Optimization of a GCaMP calcium indicator for neural activity imaging. J.Neurosci. (2012)

Release Date

2012-06-20

Peptides

Myosin light chain kinase, Green fluorescent protein, Calmodulin-1 chimera: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Myosin light chain kinase, Green fluorescent protein, Calmodulin-1 chimera