SMTL ID : 7kyc.1

Structure of the S. cerevisiae phosphatidylcholine flippase Dnf1-Lem3 complex in the E2P state

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

1 x NAG- NAG- MAN: alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-MAN.1: 12 residues within 4Å: Chain A: S.584, Y.585 Chain B: F.152, K.154, N.240, Y.288, K.291, M.292, H.347, W.348, P.349, E.352 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:K.154 Hydrophobic interactions: A:Y.585

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.2: 5 residues within 4Å: Chain B: Q.246, T.248, T.253, S.254, N.256 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 5 residues within 4Å: Chain B: S.258, T.260, I.329, N.330, N.332 No protein-ligand interaction detected (PLIP)

1 x BEF: BERYLLIUM TRIFLUORIDE ION(Covalent)

BEF.4: 10 residues within 4Å: Chain A: D.439, G.440, D.667, K.668, T.669, T.989, G.990, K.1110, N.1133 Ligands: MG.5 No protein-ligand interaction detected (PLIP)

1 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 5 residues within 4Å: Chain A: K.436, D.667, T.669, D.1130 Ligands: BEF.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.667, A:T.669, A:D.1130, A:D.1130

3 x POV: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate(Non-covalent)

POV.6: 15 residues within 4Å: Chain A: V.245, I.250, I.253, Q.610, S.611, I.615, S.616, I.619, M.1222, M.1223, N.1226, L.1227, A.1228, I.1235 Ligands: POV.7 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:V.245, A:I.250, A:I.253, A:I.615, A:I.619, A:L.1227, A:L.1227, A:L.1227, A:A.1228, A:I.1235 Hydrogen bonds: A:L.1227 POV.7: 17 residues within 4Å: Chain A: I.253, K.257, E.622, I.623, T.626, A.627, A.630, F.631, Y.633, G.634, L.1232 Chain B: R.51, R.52, P.53, K.54 Ligands: POV.6, POV.8 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:I.253, A:K.257, A:E.622, A:T.626, A:A.627, A:A.630, A:F.631, A:L.1232 Hydrogen bonds: B:K.54 POV.8: 12 residues within 4Å: Chain A: I.256, I.260, R.264, T.626, A.629, A.630, Y.633, T.648, P.649, W.652 Chain B: R.51 Ligands: POV.7 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:I.256, A:I.260, A:T.626, A:A.630, A:W.652 Hydrogen bonds: A:Y.633, B:R.51 Salt bridges: A:R.264

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

NAG.9: 5 residues within 4Å: Chain B: D.295, N.298, E.299, T.300, N.301 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.300 NAG.10: 3 residues within 4Å: Chain B: T.112, N.113, E.124 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.124

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bai, L. et al., Transport mechanism of P4 ATPase phosphatidylcholine flippases. Elife (2020)

Release Date

2021-01-06

Peptides

Phospholipid-transporting ATPase DNF1: A
Alkylphosphocholine resistance protein LEM3: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Membrane

We predict this structure to be a membrane protein.
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Phospholipid-transporting ATPase DNF1

Alkylphosphocholine resistance protein LEM3

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