SMTL ID : 7pem.1

Cryo-EM structure of phophorylated Drs2p-Cdc50p in a PS and ATP-bound E2P state

Coordinates

PDB Format

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: 7 residues within 4Å: Chain B: D.214, Y.215, N.216, L.217, T.218, N.288, A.291 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain B: V.205, D.214, N.216 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: 7 residues within 4Å: Chain B: N.199, P.245, N.246, K.249, N.305, Y.306, L.310 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.310 Hydrogen bonds: B:N.246

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)

2Y5.4: 12 residues within 4Å: Chain A: W.1028, G.1096, N.1100, F.1103, A.1106, K.1149, R.1219, W.1223, K.1224, K.1227, Y.1235, H.1236 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:W.1028, A:W.1028, A:F.1103, A:A.1106, A:W.1223 Hydrogen bonds: A:W.1223, A:K.1224, A:K.1227, A:Y.1235, A:Y.1235 Salt bridges: A:K.1149, A:K.1224, A:H.1236

1 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 5 residues within 4Å: Chain A: D.560, T.562, G.563, D.954, D.958 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.562, A:D.954, H2O.1, H2O.1

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

ATP.6: 15 residues within 4Å: Chain A: D.654, E.655, F.698, S.700, K.703, R.704, M.705, K.721, G.722, A.723, T.756, L.757, R.838, E.840, R.928 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.700, A:K.721, A:K.721, A:E.840 Salt bridges: A:R.838, A:R.928 pi-Stacking: A:F.698

1 x Q3G: O-[(R)-[(2S)-2-(hexadecanoyloxy)-3-(octadecanoyloxy)propoxy](hydroxy)phosphoryl]-D-serine(Non-covalent)

Q3G.7: 15 residues within 4Å: Chain A: T.253, I.508, S.509, V.512, L.516, S.1047, F.1048, N.1050, L.1051, F.1052, V.1055, W.1056, F.1171, F.1175, F.1183 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:V.512, A:L.516, A:F.1048, A:F.1048, A:L.1051, A:F.1052, A:V.1055, A:W.1056, A:F.1171, A:F.1171, A:F.1175, A:F.1183 Hydrogen bonds: A:N.504, A:N.1050

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, Y. et al., Substrate Transport and Specificity in a Phospholipid Flippase. To Be Published

Release Date

2022-08-24

Peptides

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

Cell division control protein 50

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