SMTL ID : 7f05.2 (1 other biounit)

Crystal structure of human cardiac calsequestrin bound with calcium

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

36 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.1: 6 residues within 4Å: Chain A: E.114, E.128, D.130, E.263, E.266 Ligands: CA.2 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.114, A:E.128, A:D.130, A:E.263, H2O.1 CA.2: 5 residues within 4Å: Chain A: E.114, S.117, D.130, E.266 Ligands: CA.1 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.114, A:E.266, H2O.1, H2O.6, H2O.7 CA.3: 2 residues within 4Å: Chain A: D.136 Chain B: D.136 5 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: A:D.136, B:D.136, H2O.5, H2O.15, H2O.17 CA.4: 6 residues within 4Å: Chain A: E.140, D.144 Chain B: E.279, D.313 Ligands: CA.5, CA.18 5 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:E.279, A:E.140, A:D.144, H2O.6, H2O.11 CA.5: 4 residues within 4Å: Chain A: D.144, E.147 Chain B: E.279 Ligands: CA.4 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.144, A:E.147, H2O.1, H2O.7, H2O.16 CA.6: 2 residues within 4Å: Chain A: E.188, E.191 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.188, A:E.191, A:E.191, H2O.7, H2O.9 CA.7: 2 residues within 4Å: Chain A: S.212, E.217 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:S.212, A:E.217, H2O.3, H2O.4, H2O.9 CA.8: 3 residues within 4Å: Chain A: E.222, T.252, T.300 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.222, A:E.222, A:T.252, H2O.3, H2O.7 CA.9: 3 residues within 4Å: Chain A: N.233, P.235, E.240 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:N.233, A:P.235, A:E.240, H2O.8, H2O.8 CA.10: 2 residues within 4Å: Chain A: E.266, D.268 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.266, A:D.268, H2O.9 CA.11: 3 residues within 4Å: Chain A: E.279 Chain B: D.144, E.147 5 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:E.147, A:E.279, A:E.279, H2O.8, H2O.16 CA.12: 6 residues within 4Å: Chain A: E.279, S.281, D.313 Chain B: E.140, D.144 Ligands: CA.35 5 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:E.140, B:D.144, A:E.279, A:D.313, H2O.2 CA.13: 3 residues within 4Å: Chain A: D.282, D.284 Chain B: E.151 5 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: B:E.151, A:D.282, H2O.1, H2O.6, H2O.10 CA.14: 2 residues within 4Å: Chain A: D.284 Chain B: E.151 5 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: B:E.151, A:D.284, H2O.1, H2O.5, H2O.12 CA.15: 5 residues within 4Å: Chain A: D.284, E.287, D.353, D.354 Chain B: E.158 5 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:E.158, A:D.284, A:D.353, A:D.354, H2O.3 CA.16: 4 residues within 4Å: Chain A: D.36, V.38, E.78, E.82 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.36, A:V.38, A:E.78, H2O.6, H2O.8 CA.17: 1 residues within 4Å: Chain B: D.313 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.313, H2O.9 CA.18: 3 residues within 4Å: Chain A: E.140, D.144 Ligands: CA.4 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.140, A:E.140, H2O.2, H2O.7 CA.19: 1 residues within 4Å: Chain A: D.113 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.113, H2O.4 CA.20: 2 residues within 4Å: Chain A: E.266 Chain B: E.24 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.266 CA.21: 1 residues within 4Å: Chain A: D.313 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.313, H2O.8, H2O.8 CA.22: 1 residues within 4Å: Chain A: E.363 No protein-ligand interaction detected (PLIP) CA.23: 4 residues within 4Å: Chain A: E.151 Chain B: D.282, D.284 Ligands: CA.24 5 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: A:E.151, B:D.282, H2O.5, H2O.11, H2O.16 CA.24: 3 residues within 4Å: Chain A: E.151 Chain B: D.284 Ligands: CA.23 5 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: A:E.151, B:D.284, H2O.4, H2O.11, H2O.13 CA.25: 5 residues within 4Å: Chain A: E.158 Chain B: D.284, E.287, D.353, D.354 6 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: A:E.158, B:D.284, B:E.287, B:D.353, B:D.354, H2O.12 CA.26: 4 residues within 4Å: Chain B: D.36, V.38, E.78, E.82 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:V.38, B:E.78, B:E.82, H2O.14, H2O.16 CA.27: 4 residues within 4Å: Chain B: E.114, E.128, D.130, E.263 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.114, B:E.128, B:D.130, B:E.263 CA.28: 4 residues within 4Å: Chain B: E.114, S.117, D.130, E.266 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.130, B:E.266, H2O.12, H2O.16, H2O.16 CA.29: 2 residues within 4Å: Chain B: E.188, E.191 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.188, B:E.191, H2O.10, H2O.14, H2O.17 CA.30: 3 residues within 4Å: Chain B: S.212, K.214, E.217 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.212, B:E.217, H2O.14, H2O.16 CA.31: 4 residues within 4Å: Chain B: N.233, K.234, P.235, E.240 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:N.233, B:P.235 CA.32: 3 residues within 4Å: Chain B: E.222, T.252, T.300 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.222, B:T.252, B:T.300, H2O.13, H2O.14 CA.33: 3 residues within 4Å: Chain B: D.298, E.360, E.363 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.298, B:E.363, H2O.10 CA.34: 1 residues within 4Å: Chain B: E.367 No protein-ligand interaction detected (PLIP) CA.35: 3 residues within 4Å: Chain B: E.140, D.144 Ligands: CA.12 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:E.140, H2O.2, H2O.4, H2O.11, H2O.16 CA.36: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fan, X.X. et al., Ca2+-dependent Formation of a Non-transmembrane Channel in a Calsequestrin-2 Dimer. To Be Published

Release Date

2022-06-08

Peptides

Calsequestrin-2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Calsequestrin-2

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