SMTL ID : 7oh5.1

Cryo-EM structure of Drs2p-Cdc50p in the E1-AlFx-ADP state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 8 residues within 4Å: Chain B: D.214, Y.215, N.216, L.217, T.218, N.288, S.290 Ligands: NAG-NAG.2 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain B: D.214, N.216 Ligands: NAG-NAG.1 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- BMA: beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-BMA.3: 8 residues within 4Å: Chain B: N.199, P.245, N.246, K.249, K.250, N.305, Y.306, L.310 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.310

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

MG.4: 1 residues within 4Å: Ligands: ADP.7 No protein-ligand interaction detected (PLIP) MG.6: 4 residues within 4Å: Chain A: D.560, T.562, D.954 Ligands: ALF.5 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.560, A:T.562, A:D.954, H2O.1, H2O.1

1 x ALF: TETRAFLUOROALUMINATE ION(Non-covalent)

ALF.5: 11 residues within 4Å: Chain A: D.560, K.561, T.562, L.834, T.835, G.836, K.934, D.954, N.957 Ligands: MG.6, ADP.7 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.560

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

ADP.7: 18 residues within 4Å: Chain A: D.560, T.562, D.654, E.655, F.698, K.703, M.705, K.721, G.722, A.723, R.755, T.756, L.757, T.835, G.836, D.837 Ligands: MG.4, ALF.5 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:T.562, A:T.562, A:T.562, A:T.562, A:E.655, A:K.721, A:R.755, A:G.836, A:G.836, A:D.837, A:D.837 Salt bridges: A:K.703, A:R.755 pi-Stacking: A:F.698, A:F.698

1 x 2Y5: (2R)-1-{[(R)-hydroxy{[(1R,2R,3R,4R,5S,6R)-2,3,5,6-tetrahydroxy-4-(phosphonooxy)cyclohexyl]oxy}phosphoryl]oxy}-3-(octadecanoyloxy)propan-2-yl (5Z,8Z,11Z,14Z)-icosa-5,8,11,14-tetraenoate(Non-covalent)

2Y5.8: 14 residues within 4Å: Chain A: W.1028, G.1096, I.1099, F.1103, A.1106, I.1110, K.1149, F.1215, R.1219, W.1223, K.1224, K.1227, Y.1235, H.1236 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:W.1028, A:F.1103, A:I.1110, A:F.1215, A:R.1219, A:W.1223, A:W.1223, A:W.1223 Hydrogen bonds: A:W.1223, A:W.1223, A:K.1224, A:Y.1235, A:Y.1235 Salt bridges: A:K.1149, A:R.1219, A:R.1219, A:R.1219, A:K.1224, A:H.1236

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.9: 2 residues within 4Å: Chain B: K.235, N.237 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.239, B:S.239

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Timcenko, M. et al., Structural basis of substrate-independent phosphorylation in a P4-ATPase lipid flippase. J.Mol.Biol. (2021)

Release Date

2021-06-09

Peptides

Probable phospholipid-transporting ATPase DRS2,Probable phospholipid-transporting ATPase DRS2: A
Cell division control protein 50: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

Membrane

We predict this structure to be a membrane protein.
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Probable phospholipid-transporting ATPase DRS2,Probable phospholipid-transporting ATPase DRS2

Cell division control protein 50

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