SMTL ID : 5a3q.1

Crystal structure of the (SR) Calcium ATPase E2-vanadate complex bound to thapsigargin and TNP-AMPPCP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.05 Å

Oligo State

monomer

Ligands

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)

TG1.1: 17 residues within 4Å: Chain A: K.253, L.254, E.256, F.257, Q.260, L.261, I.762, I.766, V.770, V.773, V.774, P.828, L.829, I.830, F.835, Y.838, M.839 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:L.254, A:F.257, A:F.257, A:Q.260, A:L.261, A:I.762, A:I.766, A:V.770, A:V.773, A:V.773, A:V.774, A:P.828, A:L.829, A:I.830, A:F.835, A:F.835, A:Y.838 Hydrogen bonds: A:L.829, A:I.830, A:I.830

1 x VN4: oxido(dioxo)vanadium(Non-covalent)

VN4.2: 10 residues within 4Å: Chain A: T.182, G.183, D.352, K.353, T.354, T.626, G.627, K.685, N.707 Ligands: MG.4 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:G.183, A:K.353, A:T.354, A:T.354, A:T.626, A:G.627, A:K.685, A:N.707 Water bridges: A:D.628

1 x DL5: Spiro(2,4,6-trinitrobenzene[1,2a]-O2',O3'-methylene-adenosine (beta,gamma-methylene)triphosphate(Non-covalent)

DL5.3: 21 residues within 4Å: Chain A: R.175, V.186, S.187, V.188, I.189, K.206, M.362, E.440, T.442, E.443, F.488, K.493, S.494, M.495, K.516, G.517, A.518, R.561, N.629, R.679 Ligands: MG.5 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:I.189, A:K.206, A:R.561, A:R.561, A:R.679 Salt bridges: A:K.206 pi-Stacking: A:F.488 pi-Cation interactions: A:R.561

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 6 residues within 4Å: Chain A: G.183, D.352, T.354, D.704, D.708 Ligands: VN4.2 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 MG.5: 2 residues within 4Å: Chain A: N.629 Ligands: DL5.3 No protein-ligand interaction detected (PLIP)

1 x K: POTASSIUM ION(Non-covalent)

K.6: 6 residues within 4Å: Chain A: Q.245, L.712, K.713, A.715, G.718, E.733 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:L.712, A:K.713, A:A.715, A:E.733, A:E.733

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.7: 3 residues within 4Å: Chain A: N.629, K.630, R.679 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Clausen, J.D. et al., Crystal Structure of the Vanadate-Inhibited Ca(2+)-ATPase. Structure (2016)

Release Date

2016-04-13

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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