SMTL ID : 6lcp.1

Cryo-EM structure of Dnf1 from Chaetomium thermophilum in the E2P state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

1 x MAN- MAN: alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose(Non-covalent)

MAN-MAN.1: 4 residues within 4Å: Chain A: A.522, W.523, Y.526 Ligands: NAG-NAG-BMA-MAN.3 No protein-ligand interaction detected (PLIP)

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

NAG-NAG-BMA.2: 5 residues within 4Å: Chain B: G.185, N.189, H.198, G.202, T.203 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN: alpha-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-MAN.3: 11 residues within 4Å: Chain A: W.523, F.524 Chain B: R.136, N.219, P.270, N.271, R.274, N.331, F.332, D.333 Ligands: MAN-MAN.1 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.524

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

NAG-NAG.4: 7 residues within 4Å: Chain B: R.238, P.239, N.241, N.314, D.315, T.316, H.317 No protein-ligand interaction detected (PLIP)

1 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 6 residues within 4Å: Chain A: D.606, G.609, D.1057, G.1058, D.1061 Ligands: BEF.6 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.606, A:D.1061

1 x BEF: BERYLLIUM TRIFLUORIDE ION(Covalent)

BEF.6: 11 residues within 4Å: Chain A: K.369, D.372, G.373, D.606, K.607, T.608, G.609, K.1037, N.1060, D.1061 Ligands: MG.5 No protein-ligand interaction detected (PLIP)

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

POV.7: 13 residues within 4Å: Chain A: P.163, V.166, Q.549, N.550, I.554, S.555, I.1149, L.1150, N.1153, L.1154, F.1155, S.1158, V.1159 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.166, A:L.1154, A:F.1155 Hydrogen bonds: A:N.550, A:N.1153, A:N.1153, A:S.1158 POV.8: 12 residues within 4Å: Chain A: K.174, I.177, R.181, E.561, I.562, T.565, L.566, A.568, F.569, Y.572, I.587, W.591 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:K.174, A:I.177, A:E.561, A:I.562, A:I.562, A:T.565, A:L.566 Salt bridges: A:R.181

1 x P5S: O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine(Non-covalent)

P5S.9: 15 residues within 4Å: Chain A: R.1109, E.1113, K.1196, L.1199, Y.1200, D.1203, Y.1206, N.1257, Y.1259, R.1320, V.1323, K.1324, Q.1327, K.1328, Y.1333 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:D.1203, A:Y.1206 Hydrogen bonds: A:E.1113, A:E.1113, A:K.1196, A:K.1196, A:Y.1333 Salt bridges: A:R.1109, A:R.1320, A:R.1320, A:K.1324, A:K.1328, A:K.1328

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

NAG.10: 4 residues within 4Å: Chain B: N.131, Y.278, Q.281, N.283 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.278, B:N.283 NAG.11: 1 residues within 4Å: Chain B: N.241 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

He, Y. et al., Structures of a P4-ATPase lipid flippase in lipid bilayers. Protein Cell (2020)

Release Date

2020-04-29

Peptides

Phospholipid-transporting ATPase: A
Cdc50: 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

Cdc50

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