SMTL ID : 3v1w.2 (1 other biounit)

Molecular Basis for Multiple Ligand Binding of Calsequestrin and Potential Inhibition by Caffeine and Gallocatecin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.91 Å

Oligo State

homo-dimer

Ligands

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 3 residues within 4Å: Chain A: N.316, D.319 Ligands: NA.10 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain B: N.316, D.319 Ligands: NA.20 No protein-ligand interaction detected (PLIP)

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

MPD.2: 7 residues within 4Å: Chain A: W.242, Y.298, W.299, A.320 Chain B: L.4, F.6, P.7 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:W.242, A:W.242, A:A.320, B:L.4, B:F.6 MPD.3: 4 residues within 4Å: Chain A: N.276, N.279, L.343, E.344 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:E.344 MPD.12: 7 residues within 4Å: Chain A: L.4, 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:L.4, A:F.6 Hydrogen bonds: B:Y.298 MPD.13: 4 residues within 4Å: Chain B: N.276, N.279, L.343, E.344 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:E.344

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

MRD.4: 8 residues within 4Å: Chain A: L.294, L.295 Chain B: P.7, E.8, Y.9, L.60, Q.63, V.64 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:L.294, B:L.60, B:Q.63 Hydrogen bonds: A:L.294 MRD.14: 8 residues within 4Å: Chain A: P.7, E.8, Y.9, L.60, Q.63, V.64 Chain B: L.294, L.295 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:L.60, A:Q.63, B:L.294 Hydrogen bonds: B:L.294

8 x CA: CALCIUM ION(Non-covalent)

CA.5: 7 residues within 4Å: Chain A: N.17, V.18, L.74, V.75, D.76, K.79, 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.1 CA.6: 3 residues within 4Å: Chain A: E.199, T.229, T.277 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.199, A:E.199, A:T.229, A:T.277, H2O.15 CA.7: 1 residues within 4Å: Chain A: T.189 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:T.189, H2O.1, H2O.4, H2O.5, H2O.15 CA.8: 4 residues within 4Å: Chain A: D.210, P.212, N.213, E.217 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.210, A:E.217, H2O.7, H2O.18, H2O.20 CA.15: 7 residues within 4Å: Chain B: N.17, V.18, L.74, V.75, D.76, K.79, 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.20 CA.16: 3 residues within 4Å: Chain B: E.199, T.229, T.277 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.199, B:E.199, B:T.229, B:T.277, H2O.35 CA.17: 1 residues within 4Å: Chain B: T.189 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:T.189, H2O.21, H2O.23, H2O.25, H2O.35 CA.18: 4 residues within 4Å: Chain B: D.210, P.212, N.213, E.217 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.210, B:E.217, H2O.26, H2O.37, H2O.40

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

NA.9: 1 residues within 4Å: Chain A: P.172 No protein-ligand interaction detected (PLIP) NA.10: 5 residues within 4Å: Chain A: G.248, N.316, V.317, T.318 Ligands: NAG-NAG.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.318, A:T.318, A:T.318 NA.19: 1 residues within 4Å: Chain B: P.172 2 PLIP interactions: 2 interactions with chain B Water bridges: B:P.172, B:I.174 NA.20: 5 residues within 4Å: Chain B: G.248, N.316, V.317, T.318 Ligands: NAG-NAG.11 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.318, B:T.318

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Subramanian, A.K. et al., Molecular Basis for Multiple Ligand Binding of Calsequestrin and Potential Inhibition by Caffeine and Gallocatecin. To be Published

Release Date

2012-12-12

Peptides

Calsequestrin-1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Calsequestrin-1

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