SMTL ID : 9dzu.1

Cryo-EM structure of the C. neoformans lipid flippase Apt1-Cdc50 bound with butyrolactol A in the E2P 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(Post Translational Modification)

NAG-NAG.1: 2 residues within 4Å: Chain A: D.88, N.129 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 6 residues within 4Å: Chain A: N.231, Q.236, T.237, Y.238, N.239, E.315 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.231

1 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-4)-alpha-D-mannopyranose-(1-6)-[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-MAN-MAN.2: 17 residues within 4Å: Chain A: V.135, G.136, R.201, Y.206, N.214, N.218, P.270, N.271, L.274, N.329, Y.330, P.331, Q.334 Chain B: Y.448, F.452, A.453, D.454 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.331 Hydrogen bonds: A:R.201, A:Y.206

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

NAG.4: 3 residues within 4Å: Chain A: Q.234, N.235, R.323 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.234, A:R.323, A:R.323

1 x BEF: BERYLLIUM TRIFLUORIDE ION(Covalent)

BEF.5: 7 residues within 4Å: Chain B: D.535, K.536, T.537, T.859, G.860, N.1016 Ligands: MG.6 No protein-ligand interaction detected (PLIP)

1 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 5 residues within 4Å: Chain B: D.535, T.537, D.1013, D.1017 Ligands: BEF.5 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.535, B:T.537, B:D.1013

1 x 01: (3R,4R,5S)-3,4-dihydroxy-5-[(1R,2R,3S,4S,5R,6R,10E,14Z,16E,18Z)-1,2,3,4,5-pentahydroxy-6,20,20-trimethylhenicosa-10,14,16,18-tetraen-1-yl]oxolan-2-one

01.7: 13 residues within 4Å: Chain B: P.127, I.130, I.134, Q.476, N.477, I.481, S.482, I.485, A.489, I.493, N.1109, V.1110, I.1118 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:I.130, B:I.485, B:A.489, B:I.493, B:I.1118 Hydrogen bonds: B:S.482, B:S.482, B:S.482, B:N.1109

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, X. et al., Butyrolactol A is a phospholipid flippase inhibitor that potentiates the bioactivity of caspofungin against resistant fungi. Biorxiv (2025)

Release Date

2025-02-05

Peptides

Transcription regulator: A
Phospholipid-transporting ATPase: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

Membrane

We predict this structure to be a membrane protein.
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Transcription regulator

Phospholipid-transporting ATPase

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