SMTL ID : 7bcw.1

Structure of MsbA in Salipro with ADP vanadate

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

2 x VO4: VANADATE ION(Non-covalent)

VO4.1: 13 residues within 4Å: Chain A: R.393, S.394, G.395, K.398, S.399, Q.440, H.553 Chain B: S.498, G.499, G.500, A.526 Ligands: ADP.2, MG.3 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:K.398, A:K.398, A:K.398, A:H.553, B:S.498, B:G.500 VO4.5: 13 residues within 4Å: Chain A: S.498, G.500, A.526 Chain B: R.393, S.394, G.395, K.398, S.399, Q.440, E.522, H.553 Ligands: ADP.6, MG.7 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Q.440, B:E.522, B:E.522, A:S.498, A:G.500

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.2: 18 residues within 4Å: Chain A: D.133, Y.367, R.370, S.394, G.395, S.396, G.397, K.398, S.399, T.400, Y.409 Chain B: V.495, L.496, L.497, S.498, Q.501 Ligands: VO4.1, MG.3 13 PLIP interactions: 10 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:D.133, A:D.133, A:S.394, A:G.395, A:K.398, A:S.399, A:T.400, B:S.498, B:Q.501, B:Q.501 Salt bridges: A:K.398 pi-Stacking: A:Y.367, A:Y.367 ADP.6: 16 residues within 4Å: Chain A: V.495, L.496, S.498, Q.501 Chain B: D.133, Y.367, G.395, S.396, G.397, K.398, S.399, T.400, Y.409, Q.440 Ligands: VO4.5, MG.7 12 PLIP interactions: 9 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:D.133, B:G.395, B:K.398, B:S.399, B:S.399, B:T.400, B:Y.409, A:S.498, A:Q.501, A:Q.501 pi-Stacking: B:Y.367, B:Y.367

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: S.399, Q.440, D.521 Ligands: VO4.1, ADP.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:S.399 MG.7: 4 residues within 4Å: Chain B: S.399, Q.440 Ligands: VO4.5, ADP.6 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:S.399

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

POV.4: 13 residues within 4Å: Chain A: T.25, V.162, V.163, A.167, I.169, F.173, A.191, V.194, S.195, I.198, L.314, L.317, N.321 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:T.25, A:V.162, A:I.198, A:L.317 POV.8: 8 residues within 4Å: Chain B: I.169, F.173, A.191, V.194, S.195, I.198, L.310, L.314 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:I.198

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kehlenbeck, D.M. et al., Cryo-EM structure of MsbA in saposin-lipid nanoparticles (Salipro) provides insights into nucleotide coordination. Febs J. (2022)

Release Date

2022-01-12

Peptides

ATP-dependent lipid A-core flippase: AB

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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ATP-dependent lipid A-core flippase