SMTL ID : 5xaa.1

Complete structure factors and an atomic model of the calcium pump (SERCA1A) and associated phospholipids in the E2-ALF-(TG) crystals of P21212 symmetry

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

monomer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: D.352, T.354, D.704, D.708 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.1, H2O.1

1 x ALF: TETRAFLUOROALUMINATE ION(Non-covalent)

ALF.2: 13 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, D.708 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: 20 residues within 4Å: Chain A: K.253, L.254, E.256, F.257, Q.260, L.261, V.264, I.268, A.307, I.766, N.769, V.770, V.773, V.774, F.777, L.829, I.830, F.835, Y.838 Ligands: PCW.22 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:K.253, A:L.254, A:F.257, A:F.257, A:F.257, A:Q.260, A:V.264, A:I.268, A:I.766, A:N.769, A:V.770, A:V.773, A:V.773, A:V.774, A:F.777, A:L.829, A:I.830, A:I.830, A:Y.838 Hydrogen bonds: A:L.829, A:I.830

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

PCW.4: 2 residues within 4Å: Chain A: L.50 Ligands: PCW.6 Ligand excluded by PLIP PCW.5: 2 residues within 4Å: Chain A: S.288, W.289 Ligand excluded by PLIP PCW.6: 2 residues within 4Å: Chain A: W.108 Ligands: PCW.4 Ligand excluded by PLIP PCW.7: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP PCW.8: 5 residues within 4Å: Chain A: R.64, E.259, S.262, S.266 Ligands: PCW.11 Ligand excluded by PLIP PCW.9: 4 residues within 4Å: Chain A: G.832, W.833, L.993 Ligands: PCW.28 Ligand excluded by PLIP PCW.10: 2 residues within 4Å: Chain A: F.58 Ligands: PCW.33 Ligand excluded by PLIP PCW.11: 3 residues within 4Å: Chain A: R.64, L.68 Ligands: PCW.8 Ligand excluded by PLIP PCW.12: 4 residues within 4Å: Chain A: W.108, T.318, A.321, R.325 Ligand excluded by PLIP PCW.13: 2 residues within 4Å: Chain A: W.51, E.52 Ligand excluded by PLIP PCW.14: 2 residues within 4Å: Chain A: F.987 Ligands: PCW.15 Ligand excluded by PLIP PCW.15: 2 residues within 4Å: Chain A: Y.992 Ligands: PCW.14 Ligand excluded by PLIP PCW.16: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP PCW.17: 1 residues within 4Å: Ligands: PCW.18 Ligand excluded by PLIP PCW.18: 4 residues within 4Å: Chain A: W.78 Ligands: PCW.17, PCW.19, PCW.20 Ligand excluded by PLIP PCW.19: 3 residues within 4Å: Chain A: V.75, F.79 Ligands: PCW.18 Ligand excluded by PLIP PCW.20: 3 residues within 4Å: Chain A: W.78 Ligands: PCW.18, PCW.35 Ligand excluded by PLIP PCW.21: 5 residues within 4Å: Chain A: Q.260, K.263, V.264, L.267 Ligands: PCW.22 Ligand excluded by PLIP PCW.22: 4 residues within 4Å: Chain A: E.256, F.835 Ligands: TG1.3, PCW.21 Ligand excluded by PLIP PCW.23: 3 residues within 4Å: Chain A: M.858, Y.859 Ligands: PCW.31 Ligand excluded by PLIP PCW.24: 1 residues within 4Å: Ligands: PCW.25 Ligand excluded by PLIP PCW.25: 1 residues within 4Å: Ligands: PCW.24 Ligand excluded by PLIP PCW.26: 4 residues within 4Å: Chain A: T.85, I.86, A.88, M.956 Ligand excluded by PLIP PCW.27: 5 residues within 4Å: Chain A: I.275, G.278, H.279, T.872, H.873 Ligand excluded by PLIP PCW.28: 4 residues within 4Å: Chain A: G.832, W.833, F.836 Ligands: PCW.9 Ligand excluded by PLIP PCW.29: 2 residues within 4Å: Chain A: Y.950 Ligands: PCW.30 Ligand excluded by PLIP PCW.30: 2 residues within 4Å: Chain A: L.965 Ligands: PCW.29 Ligand excluded by PLIP PCW.31: 4 residues within 4Å: Chain A: Y.859, E.861, K.973 Ligands: PCW.23 Ligand excluded by PLIP PCW.32: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP PCW.33: 2 residues within 4Å: Chain A: I.55 Ligands: PCW.10 Ligand excluded by PLIP PCW.34: 1 residues within 4Å: Chain A: W.933 Ligand excluded by PLIP PCW.35: 2 residues within 4Å: Chain A: F.89 Ligands: PCW.20 Ligand excluded by PLIP PCW.36: 0 residues within 4Å: (No contacts) 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

2017-05-24

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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