SMTL ID : 7bt2.1

Crystal structure of the SERCA2a in the E2.ATP state

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

monomer

Ligands

1 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 19 residues within 4Å: Chain A: D.351, K.352, T.353, E.439, E.442, F.487, R.489, K.492, M.494, K.514, G.515, A.516, R.559, C.560, L.561, T.624, G.625, D.626, R.677 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:K.352, A:T.353, A:T.353, A:E.439, A:K.514, A:A.516, A:R.559, A:C.560, A:G.625, A:G.625, A:R.677 Water bridges: A:D.351, A:R.489, A:R.489, A:R.559, A:I.623 Salt bridges: A:R.489, A:R.559

1 x K: POTASSIUM ION(Non-covalent)

K.2: 5 residues within 4Å: Chain A: L.710, K.711, A.713, G.716, E.731 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:L.710, A:K.711, A:A.713, A:E.731

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

PCW.3: 8 residues within 4Å: Chain A: K.252, F.256, Q.259, L.260, K.824, P.826, L.827, I.828 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.256, A:L.260 Hydrogen bonds: A:L.827, A:I.828 PCW.4: 3 residues within 4Å: Chain A: G.830, W.831, L.991 No protein-ligand interaction detected (PLIP) PCW.5: 3 residues within 4Å: Chain A: L.922, F.985, R.988 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.922 Salt bridges: A:R.988 PCW.6: 1 residues within 4Å: Chain A: R.324 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.324

1 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.7: 8 residues within 4Å: Chain A: T.499, P.500, K.502, P.503, S.504, T.506, S.507, M.508 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:T.499, A:M.508 Hydrogen bonds: A:S.504, A:S.504, A:S.509

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kabashima, Y. et al., What ATP binding does to the Ca2+pump and how nonproductive phosphoryl transfer is prevented in the absence of Ca2. Proc.Natl.Acad.Sci.USA (2020)

Release Date

2020-07-15

Peptides

Sarcoplasmic/endoplasmic reticulum calcium ATPase 2: 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 2