SMTL ID : 3w5a.1

Crystal structure of the calcium pump and sarcolipin from rabbit fast twitch skeletal muscle in the E1.Mg2+ state

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.01 Å

Oligo State

hetero-2-1-mer

Ligands

2 x TM1: 2',3'-O-[(1r)-2,4,6-trinitrocyclohexa-2,5-diene-1,1-diyl]adenosine 5'-(dihydrogen phosphate)(Non-covalent)

TM1.1: 16 residues within 4Å: Chain A: T.354, F.488, R.490, K.493, M.495, K.516, G.517, A.518, R.561, L.563, T.626, G.627, R.679, V.680, E.681 Ligands: MG.5 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:T.354, A:R.490, A:R.561, A:T.626, A:G.627, A:E.681 Water bridges: A:T.354 pi-Stacking: A:F.488 TM1.7: 13 residues within 4Å: Chain B: T.354, F.488, R.490, K.493, M.495, K.516, R.561, L.563, G.627, R.679, V.680, E.681 Ligands: MG.12 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.354, B:R.490, B:R.561, B:G.627, B:E.681 pi-Stacking: B:F.488

5 x PTY: PHOSPHATIDYLETHANOLAMINE(Non-covalent)

PTY.2: 5 residues within 4Å: Chain A: S.831, G.832, W.833, F.836, L.993 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.836 Hydrogen bonds: A:G.832, A:W.833 PTY.3: 4 residues within 4Å: Chain A: M.924, F.987, R.990, N.991 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.991 Salt bridges: A:R.990 PTY.8: 4 residues within 4Å: Chain B: S.831, G.832, W.833, L.993 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.832, B:W.833 PTY.9: 8 residues within 4Å: Chain B: S.922, M.924, R.925, E.983, F.987, R.990, N.991 Ligands: PTY.10 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:M.924, B:E.983 Hydrogen bonds: B:N.991 Salt bridges: B:R.990 PTY.10: 3 residues within 4Å: Chain B: F.987, Y.992 Ligands: PTY.9 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.992

4 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.4: 5 residues within 4Å: Chain A: A.306, N.769, E.772, N.797, D.801 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:A.306, A:E.772, A:D.801, H2O.1 MG.5: 1 residues within 4Å: Ligands: TM1.1 No protein-ligand interaction detected (PLIP) MG.11: 5 residues within 4Å: Chain B: A.306, N.769, E.772, N.797, D.801 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:A.306, B:E.772, B:D.801, H2O.1 MG.12: 1 residues within 4Å: Ligands: TM1.7 No protein-ligand interaction detected (PLIP)

2 x NA: SODIUM ION(Non-functional Binders)

NA.6: 4 residues within 4Å: Chain A: L.712, K.713, A.715, E.733 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.712 NA.13: 5 residues within 4Å: Chain B: L.712, K.713, A.715, E.716, E.733 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.733

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Toyoshima, C. et al., Crystal structures of the calcium pump and sarcolipin in the Mg2+-bound E1 state. Nature (2013)

Release Date

2013-03-06

Peptides

SERCA1a: AB
Sarcolipin: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Membrane

We predict this structure to be a membrane protein.
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SERCA1a

Sarcolipin

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