SMTL ID : 7kya.1

Structure of the S. cerevisiae phosphatidylcholine flippase Dnf2-Lem3 complex in the E2P state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

3 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: 3 residues within 4Å: Chain B: N.298, T.300, N.301 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain B: Q.246, T.248, T.253, N.256 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain B: S.258, T.260, N.330, N.332 No protein-ligand interaction detected (PLIP)

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.2: 12 residues within 4Å: Chain A: Y.629, F.630 Chain B: F.152, K.154, M.238, N.240, Y.288, K.291, H.347, W.348, P.349, E.352 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:Y.629, A:F.630, B:P.349 Hydrogen bonds: B:K.291

5 x CLR: CHOLESTEROL(Non-covalent)

CLR.5: 5 residues within 4Å: Chain A: L.608, T.611, F.1246, W.1247, I.1250 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.608, A:T.611, A:F.1246, A:W.1247, A:I.1250 CLR.8: 8 residues within 4Å: Chain A: F.606, F.610, K.621, A.639, S.640, F.644, F.647, W.648 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.606, A:F.610, A:F.610, A:F.644, A:F.647, A:F.647 Hydrogen bonds: A:K.621 CLR.9: 3 residues within 4Å: Chain A: I.1439, I.1442, Y.1447 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.1442, A:I.1442 CLR.10: 4 residues within 4Å: Chain A: E.1343, A.1417, P.1419, W.1422 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.1419, A:W.1422 CLR.11: 4 residues within 4Å: Chain B: L.94, I.376, I.380, I.384 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.94, B:I.380, B:I.384

1 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 5 residues within 4Å: Chain A: K.481, D.712, T.714, D.1173 Ligands: BEF.7 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:T.714, A:D.1173

1 x BEF: BERYLLIUM TRIFLUORIDE ION(Non-covalent)

BEF.7: 12 residues within 4Å: Chain A: K.481, D.484, G.485, D.712, K.713, T.714, T.1032, G.1033, K.1153, N.1176, D.1177 Ligands: MG.6 No protein-ligand interaction detected (PLIP)

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

NAG.12: 2 residues within 4Å: Chain B: N.113, E.124 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.113

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 DNF2: 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 DNF2

Alkylphosphocholine resistance protein LEM3

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