SMTL ID : 6lcr.1

Cryo-EM structure of Dnf1 from Chaetomium thermophilum in the E1-ATP 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(Non-covalent)(Post Translational Modification)

NAG-NAG.1: 4 residues within 4Å: Chain B: N.131, Y.132, Y.278, Q.281 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 5 residues within 4Å: Chain B: G.185, K.186, N.189, H.198, G.202 No protein-ligand interaction detected (PLIP)

2 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: 7 residues within 4Å: Chain A: F.524 Chain B: R.136, N.219, N.271, R.275, N.331, F.332 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.524 NAG-NAG-BMA.4: 5 residues within 4Å: Chain B: N.241, T.243, N.314, 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, T.608, D.1057, D.1061, E.1078 Ligands: ACP.6 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.606

1 x ACP: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER(Non-covalent)

ACP.6: 17 residues within 4Å: Chain A: D.606, K.607, T.608, D.739, E.740, F.781, K.786, G.805, R.839, L.918, T.919, G.920, D.921, K.1037, N.1060, E.1078 Ligands: MG.5 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:K.607, A:T.608, A:D.739, A:E.740, A:R.839, A:R.839, A:G.920, A:K.1037, A:E.1078 Salt bridges: A:R.839 pi-Stacking: A:F.781, A:F.781

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

P5S.7: 11 residues within 4Å: Chain A: E.1113, L.1199, Y.1200, D.1203, Y.1206, N.1257, P.1319, R.1320, V.1323, K.1324, Q.1327 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:L.1199, A:Y.1200, A:D.1203, A:Y.1206, A:V.1323 Hydrogen bonds: A:E.1113, A:E.1113, A:E.1113, A:K.1196 Salt bridges: A:R.1320, A:R.1320, A:R.1320, A:K.1324, A:K.1324, A:K.1328

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

NAG.8: 3 residues within 4Å: Chain B: S.224, P.239, N.241 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.224, B:N.241

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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