SMTL ID : 6yso.1 (1 other biounit)

Crystal structure of the (SR) Ca2+-ATPase solved by vanadium SAD phasing

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.13 Å

Oligo State

monomer

Ligands

1 x 128: SPIRO(2,4,6-TRINITROBENZENE[1,2A]-2O',3O'-METHYLENE-ADENINE-TRIPHOSPHATE(Non-covalent)

128.1: 19 residues within 4Å: Chain A: R.174, V.185, S.186, V.187, I.188, K.205, M.361, E.439, T.441, F.487, K.492, M.494, K.515, G.516, A.517, R.560, N.628, R.678 Ligands: MG.5 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:I.188, A:K.492, A:R.560, A:N.628 Salt bridges: A:K.205, A:R.560, A:R.678 pi-Stacking: A:F.487 pi-Cation interactions: A:R.560, A:R.560

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)

TG1.2: 18 residues within 4Å: Chain A: L.253, E.255, F.256, Q.259, L.260, I.267, A.306, I.761, I.765, N.768, V.769, V.772, F.776, L.828, I.829, F.834, Y.837, M.838 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:L.253, A:F.256, A:F.256, A:Q.259, A:I.267, A:I.761, A:I.765, A:V.769, A:V.769, A:V.772, A:F.776, A:L.828, A:I.829, A:I.829, A:I.829, A:F.834, A:Y.837

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

VN4.3: 10 residues within 4Å: Chain A: T.181, G.182, D.351, K.352, T.353, T.625, G.626, K.684, N.706 Ligands: MG.4 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:T.181, A:K.352, A:T.353, A:G.626, A:K.684, A:N.706 Water bridges: A:D.627

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 4 residues within 4Å: Chain A: D.351, T.353, D.703 Ligands: VN4.3 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.351, A:T.353, A:D.703, H2O.1, H2O.1 MG.5: 3 residues within 4Å: Chain A: R.560, N.628 Ligands: 128.1 No protein-ligand interaction detected (PLIP)

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

CL.6: 3 residues within 4Å: Chain A: N.628, K.629, R.678 Ligand excluded by PLIP

1 x K: POTASSIUM ION(Non-covalent)

K.7: 6 residues within 4Å: Chain A: Q.244, L.711, K.712, A.714, G.717, E.732 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:L.711, A:A.714, A:E.732, A:E.732

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

El Omari, K. et al., Experimental phasing with vanadium and application to nucleotide-binding membrane proteins. Iucrj (2020)

Release Date

2020-11-04

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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