SMTL ID : 5xa9.1

Complete structure factors and an atomic model of the calcium pump (SERCA1A) and associated phospholipids in the E2-ALF-(TG) crystals of C2 symmetry

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

monomer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.352, T.354, D.704 Ligands: ALF.2 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.352, A:T.354, A:D.704, H2O.2, H2O.2

1 x ALF: TETRAFLUOROALUMINATE ION(Non-covalent)

ALF.2: 12 residues within 4Å: Chain A: T.182, G.183, E.184, D.352, K.353, T.354, I.625, T.626, G.627, K.685, N.707 Ligands: MG.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.352, A:D.352, H2O.1

1 x TG1: OCTANOIC ACID [3S-[3ALPHA, 3ABETA, 4ALPHA, 6BETA, 6ABETA, 7BETA, 8ALPHA(Z), 9BALPHA]]-6-(ACETYLOXY)-2,3,-3A,4,5,6,6A,7,8,9B-DECAHYDRO-3,3A-DIHYDROXY-3,6,9-TRIMETHYL-8-[(2-METHYL-1-OXO-2-BUTENYL)OX Y]-2-OXO-4-(1-OXOBUTOXY)-AZULENO[4,5-B]FURAN-7-YL ESTER(Non-covalent)

TG1.3: 15 residues within 4Å: Chain A: L.254, E.256, F.257, Q.260, L.261, V.264, I.766, N.769, V.770, V.773, F.777, L.829, I.830, F.835, M.839 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.254, A:F.257, A:F.257, A:Q.260, A:I.766, A:I.766, A:V.770, A:V.773, A:V.773, A:F.777, A:I.830 Hydrogen bonds: A:I.830

34 x PCW: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)(Non-functional Binders)

PCW.4: 4 residues within 4Å: Chain A: E.256, Q.260, L.267 Ligands: PCW.25 Ligand excluded by PLIP PCW.5: 2 residues within 4Å: Chain A: G.832, F.836 Ligand excluded by PLIP PCW.6: 3 residues within 4Å: Chain A: N.991 Ligands: PCW.10, PCW.29 Ligand excluded by PLIP PCW.7: 6 residues within 4Å: Chain A: L.322, R.326, F.810, W.933 Ligands: PCW.11, PCW.23 Ligand excluded by PLIP PCW.8: 1 residues within 4Å: Chain A: R.111 Ligand excluded by PLIP PCW.9: 1 residues within 4Å: Ligands: PCW.30 Ligand excluded by PLIP PCW.10: 3 residues within 4Å: Chain A: N.991, Y.992 Ligands: PCW.6 Ligand excluded by PLIP PCW.11: 2 residues within 4Å: Ligands: PCW.7, PCW.22 Ligand excluded by PLIP PCW.12: 2 residues within 4Å: Chain A: F.280 Ligands: PCW.21 Ligand excluded by PLIP PCW.13: 4 residues within 4Å: Chain A: W.78, E.80, T.85, F.89 Ligand excluded by PLIP PCW.14: 7 residues within 4Å: Chain A: I.275, N.276, G.278, Y.295, G.783, T.872 Ligands: PCW.37 Ligand excluded by PLIP PCW.15: 1 residues within 4Å: Ligands: PCW.20 Ligand excluded by PLIP PCW.16: 2 residues within 4Å: Chain A: Y.859 Ligands: PCW.37 Ligand excluded by PLIP PCW.17: 5 residues within 4Å: Chain A: L.76, F.79, I.290, I.294 Ligands: PCW.31 Ligand excluded by PLIP PCW.18: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP PCW.19: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP PCW.20: 3 residues within 4Å: Chain A: L.969, K.973 Ligands: PCW.15 Ligand excluded by PLIP PCW.21: 4 residues within 4Å: Chain A: S.288, W.289 Ligands: PCW.12, PCW.31 Ligand excluded by PLIP PCW.22: 2 residues within 4Å: Chain A: I.932 Ligands: PCW.11 Ligand excluded by PLIP PCW.23: 3 residues within 4Å: Chain A: R.325 Ligands: PCW.7, PCW.36 Ligand excluded by PLIP PCW.24: 2 residues within 4Å: Chain A: R.64 Ligands: PCW.34 Ligand excluded by PLIP PCW.25: 5 residues within 4Å: Chain A: Q.260, K.263, L.267 Ligands: PCW.4, PCW.33 Ligand excluded by PLIP PCW.26: 3 residues within 4Å: Chain A: G.832, W.833, L.993 Ligand excluded by PLIP PCW.27: 2 residues within 4Å: Chain A: F.58, R.64 Ligand excluded by PLIP PCW.28: 1 residues within 4Å: Chain A: L.50 Ligand excluded by PLIP PCW.29: 3 residues within 4Å: Chain A: F.987, R.990 Ligands: PCW.6 Ligand excluded by PLIP PCW.30: 3 residues within 4Å: Chain A: W.929 Ligands: PCW.9, PCW.32 Ligand excluded by PLIP PCW.31: 2 residues within 4Å: Ligands: PCW.17, PCW.21 Ligand excluded by PLIP PCW.32: 1 residues within 4Å: Ligands: PCW.30 Ligand excluded by PLIP PCW.33: 1 residues within 4Å: Ligands: PCW.25 Ligand excluded by PLIP PCW.34: 2 residues within 4Å: Chain A: K.263 Ligands: PCW.24 Ligand excluded by PLIP PCW.35: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP PCW.36: 5 residues within 4Å: Chain A: W.108, Q.109, T.324, R.325 Ligands: PCW.23 Ligand excluded by PLIP PCW.37: 4 residues within 4Å: Chain A: L.782, Y.868 Ligands: PCW.14, PCW.16 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Norimatsu, Y. et al., Protein-phospholipid interplay revealed with crystals of a calcium pump. Nature (2017)

Release Date

2017-06-14

Peptides

Sarcoplasmic/endoplasmic reticulum calcium ATPase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Membrane

We predict this structure to be a membrane protein.
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Sarcoplasmic/endoplasmic reticulum calcium ATPase 1

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