SMTL ID : 1wpg.1

Crystal structure of the SR CA2+-ATPase with MGF4

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

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

MG.1: 4 residues within 4Å: Chain A: D.351, T.353, D.703 Ligands: MF4.4 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.351, A:T.353, A:D.703, H2O.4, H2O.5 MG.2: 2 residues within 4Å: Chain A: K.205 Ligands: ADP.5 No protein-ligand interaction detected (PLIP) MG.7: 4 residues within 4Å: Chain B: D.351, T.353, D.703 Ligands: MF4.10 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.351, B:T.353, B:D.703, H2O.11, H2O.11 MG.8: 1 residues within 4Å: Ligands: ADP.11 No protein-ligand interaction detected (PLIP) MG.13: 4 residues within 4Å: Chain C: D.351, T.353, D.703 Ligands: MF4.16 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.351, C:T.353, C:D.703, H2O.18, H2O.18 MG.14: 1 residues within 4Å: Ligands: ADP.17 No protein-ligand interaction detected (PLIP) MG.19: 4 residues within 4Å: Chain D: D.351, T.353, D.703 Ligands: MF4.22 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.351, D:T.353, D:D.703, H2O.25, H2O.25 MG.20: 2 residues within 4Å: Chain D: K.205 Ligands: ADP.23 No protein-ligand interaction detected (PLIP)

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

NA.3: 4 residues within 4Å: Chain A: L.711, K.712, A.714, E.732 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.714 NA.9: 5 residues within 4Å: Chain B: Q.244, L.711, K.712, A.714, E.732 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.244, B:E.732 NA.15: 5 residues within 4Å: Chain C: Q.244, L.711, K.712, A.714, E.732 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Q.244, C:A.714, C:G.717 NA.21: 4 residues within 4Å: Chain D: L.711, K.712, A.714, E.732 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:L.711

4 x MF4: TETRAFLUOROMAGNESATE(2-)(Non-covalent)

MF4.4: 13 residues within 4Å: Chain A: T.181, G.182, E.183, D.351, K.352, T.353, T.625, G.626, D.627, K.684, D.703, N.706 Ligands: MG.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.351 MF4.10: 12 residues within 4Å: Chain B: T.181, G.182, E.183, D.351, K.352, T.353, T.625, G.626, D.627, K.684, N.706 Ligands: MG.7 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.351 MF4.16: 12 residues within 4Å: Chain C: T.181, G.182, E.183, D.351, K.352, T.353, T.625, G.626, D.627, K.684, N.706 Ligands: MG.13 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.351 MF4.22: 12 residues within 4Å: Chain D: T.181, G.182, E.183, D.351, K.352, T.353, T.625, G.626, D.627, K.684, N.706 Ligands: MG.19 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.351

4 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.5: 11 residues within 4Å: Chain A: I.188, K.205, E.442, F.487, M.494, K.515, G.516, A.517, R.560, L.562 Ligands: MG.2 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:E.442 Water bridges: A:I.188, A:K.205, A:K.205, A:K.205, A:C.561 Salt bridges: A:K.205, A:K.205 ADP.11: 9 residues within 4Å: Chain B: I.188, K.205, F.487, M.494, K.515, G.516, A.517, L.562 Ligands: MG.8 8 PLIP interactions: 8 interactions with chain B Water bridges: B:R.174, B:R.174, B:K.205, B:K.205, B:T.441 Salt bridges: B:K.205, B:K.205, B:K.492 ADP.17: 9 residues within 4Å: Chain C: I.188, K.205, F.487, M.494, K.515, G.516, A.517, L.562 Ligands: MG.14 7 PLIP interactions: 7 interactions with chain C Water bridges: C:R.174, C:R.174, C:K.205, C:K.205 Salt bridges: C:K.205, C:K.205, C:K.492 ADP.23: 11 residues within 4Å: Chain D: I.188, K.205, E.442, F.487, M.494, K.515, G.516, A.517, R.560, L.562 Ligands: MG.20 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:E.442, D:E.442 Water bridges: D:R.174, D:I.188, D:K.205, D:K.205, D:K.205, D:T.441, D:C.561 Salt bridges: D:K.205, D:K.205

4 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)

TG1.6: 19 residues within 4Å: Chain A: K.252, L.253, E.255, F.256, Q.259, L.260, V.263, A.306, I.765, N.768, V.769, V.772, V.773, F.776, L.828, I.829, F.834, Y.837, M.838 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:L.253, A:F.256, A:F.256, A:F.256, A:Q.259, A:L.260, A:I.765, A:N.768, A:V.769, A:V.769, A:V.772, A:V.773, A:F.776, A:L.828, A:I.829, A:Y.837 Hydrogen bonds: A:E.255, A:L.828, A:I.829 TG1.12: 18 residues within 4Å: Chain B: K.252, L.253, E.255, F.256, Q.259, L.260, V.263, I.267, A.306, I.765, N.768, V.769, V.772, L.828, I.829, F.834, Y.837, M.838 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:L.253, B:F.256, B:F.256, B:F.256, B:Q.259, B:L.260, B:I.267, B:I.765, B:N.768, B:V.769, B:V.772, B:L.828, B:I.829, B:F.834, B:Y.837 Hydrogen bonds: B:E.255, B:L.828, B:I.829 TG1.18: 18 residues within 4Å: Chain C: K.252, L.253, E.255, F.256, Q.259, L.260, V.263, I.267, A.306, I.765, N.768, V.769, V.772, L.828, I.829, F.834, Y.837, M.838 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:L.253, C:F.256, C:F.256, C:F.256, C:Q.259, C:L.260, C:I.267, C:I.765, C:N.768, C:V.769, C:V.772, C:L.828, C:I.829, C:F.834, C:Y.837 Hydrogen bonds: C:L.828, C:I.829 TG1.24: 19 residues within 4Å: Chain D: K.252, L.253, E.255, F.256, Q.259, L.260, V.263, A.306, I.765, N.768, V.769, V.772, V.773, F.776, L.828, I.829, F.834, Y.837, M.838 18 PLIP interactions: 18 interactions with chain D Hydrophobic interactions: D:L.253, D:F.256, D:F.256, D:F.256, D:Q.259, D:L.260, D:I.765, D:N.768, D:V.769, D:V.769, D:V.772, D:V.773, D:F.776, D:L.828, D:I.829, D:Y.837 Hydrogen bonds: D:L.828, D:I.829

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Toyoshima, C. et al., Lumenal gating mechanism revealed in calcium pump crystal structures with phosphate analogues. Nature (2004)

Release Date

2004-10-05

Peptides

Sarcoplasmic/endoplasmic reticulum calcium ATPase 1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Membrane

We predict this structure to be a membrane protein.
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Sarcoplasmic/endoplasmic reticulum calcium ATPase 1

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