SMTL ID : 3us3.1

Recombinant rabbit skeletal calsequestrin-MPD complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.74 Å

Oligo State

homo-dimer

Ligands

6 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.1: 7 residues within 4Å: Chain A: W.242, Y.298, W.299, A.320 Chain B: D.5, F.6, P.7 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:F.6, A:W.242, A:W.242, A:A.320 Hydrogen bonds: B:D.5 MPD.3: 6 residues within 4Å: Chain A: N.279, D.281, L.282, L.343, E.344, L.347 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.343, A:L.347 Water bridges: A:N.279 MPD.4: 7 residues within 4Å: Chain A: V.314, N.316, D.321, S.322, V.346, G.349, E.350 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:N.316, A:E.350 Hydrogen bonds: A:V.314 Water bridges: A:V.346, A:G.349 MPD.10: 7 residues within 4Å: Chain A: D.5, F.6, P.7 Chain B: W.242, Y.298, W.299, A.320 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:W.242, B:W.242, B:A.320, A:F.6 Hydrogen bonds: B:Y.298, A:D.5 MPD.12: 6 residues within 4Å: Chain B: N.279, D.281, L.282, L.343, E.344, L.347 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.343, B:L.347 Water bridges: B:N.279 MPD.13: 7 residues within 4Å: Chain B: V.314, N.316, D.321, S.322, V.346, G.349, E.350 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:N.316, B:E.350 Hydrogen bonds: B:V.314 Water bridges: B:V.346, B:G.349

2 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.2: 8 residues within 4Å: Chain A: L.294, L.295 Chain B: P.7, E.8, Y.9, L.60, Q.63, V.64 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.294, B:L.60 Hydrogen bonds: A:L.294 MRD.11: 8 residues within 4Å: Chain A: P.7, E.8, Y.9, L.60, Q.63, V.64 Chain B: L.294, L.295 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:L.60, B:L.294 Hydrogen bonds: B:L.294

8 x CA: CALCIUM ION(Non-covalent)

CA.5: 6 residues within 4Å: Chain A: N.17, V.18, L.74, V.75, D.76, D.80 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:V.18, A:L.74, A:D.80, H2O.5 CA.6: 3 residues within 4Å: Chain A: E.199, T.229, T.277 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.199, A:E.199, A:T.229, A:T.277, A:T.277 CA.7: 4 residues within 4Å: Chain A: D.210, P.212, N.213, E.217 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.210, A:P.212, A:E.217, A:E.217, H2O.1 CA.8: 2 residues within 4Å: Chain A: T.189, D.196 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:T.189, A:T.189, H2O.4, H2O.8, H2O.12 CA.14: 6 residues within 4Å: Chain B: N.17, V.18, L.74, V.75, D.76, D.80 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:V.18, B:L.74, B:D.80, H2O.21 CA.15: 3 residues within 4Å: Chain B: E.199, T.229, T.277 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.199, B:E.199, B:T.229, B:T.277, B:T.277 CA.16: 4 residues within 4Å: Chain B: D.210, P.212, N.213, E.217 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.210, B:P.212, B:E.217, B:E.217, H2O.18 CA.17: 2 residues within 4Å: Chain B: T.189, D.196 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:T.189, B:T.189, H2O.21, H2O.24, H2O.29

2 x NA: SODIUM ION(Non-functional Binders)

NA.9: 2 residues within 4Å: Chain A: P.172, Y.173 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.173 NA.18: 2 residues within 4Å: Chain B: P.172, Y.173 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.173

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sanchez, E.J. et al., Glycosylation of skeletal calsequestrin: implications for its function. J.Biol.Chem. (2012)

Release Date

2011-12-21

Peptides

Calsequestrin-1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Calsequestrin-1

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