SMTL ID : 7ph4.1

AMP-PNP bound nanodisc reconstituted MsbA with nanobodies, spin-labeled at position T68C

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-mer

Ligands

2 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.1: 21 residues within 4Å: Chain A: D.128, Y.362, S.389, G.390, S.391, G.392, K.393, S.394, T.395, Y.404, Q.435, E.517, H.548 Chain B: V.490, L.491, L.492, S.493, G.494, G.495, Q.496 Ligands: MG.2 19 PLIP interactions: 13 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:D.128, A:G.390, A:S.391, A:G.392, A:K.393, A:K.393, A:S.394, A:T.395, A:Q.435, A:E.517, A:H.548, B:S.493, B:S.493, B:G.494, B:G.495, B:Q.496, B:Q.496 pi-Stacking: A:Y.362, A:Y.362 ANP.4: 22 residues within 4Å: Chain A: V.490, L.491, L.492, S.493, G.494, G.495, Q.496, A.521 Chain B: D.128, Y.362, S.389, G.390, S.391, G.392, K.393, S.394, T.395, Y.404, Q.435, E.517, H.548 Ligands: MG.5 21 PLIP interactions: 15 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:D.128, B:G.390, B:S.391, B:G.392, B:K.393, B:K.393, B:K.393, B:S.394, B:T.395, B:Q.435, B:E.517, A:S.493, A:S.493, A:G.494, A:G.495, A:Q.496, A:Q.496 Water bridges: B:S.394, B:Q.435 pi-Stacking: B:Y.362, B:Y.362

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: S.394, Q.435 Ligands: ANP.1 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.394, H2O.1, H2O.1 MG.5: 3 residues within 4Å: Chain B: S.394, Q.435 Ligands: ANP.4 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.394, H2O.1, H2O.1

2 x LMT: DODECYL-BETA-D-MALTOSIDE(Non-covalent)

LMT.3: 12 residues within 4Å: Chain A: W.21, F.24, R.25, L.27, W.28, I.31, L.38, V.103, S.104, V.107, S.150, L.154 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.24, A:F.24, A:L.27, A:L.38, A:L.38, A:V.103, A:V.107, A:L.154 Hydrogen bonds: A:R.25 LMT.6: 10 residues within 4Å: Chain B: W.21, F.24, R.25, W.28, I.31, L.38, S.104, V.107, S.150, L.154 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:F.24, B:L.38, B:V.107, B:L.154 Hydrogen bonds: B:F.24, B:R.25

2 x 88T: (1~{R},4~{R},11~{S},14~{S},19~{Z})-19-[2-[2,5-bis(oxidanylidene)pyrrolidin-1-yl]ethylimino]-7,8,17,18-tetraoxa-1,4,11,14-tetrazatricyclo[12.6.2.2^{4,11}]tetracosane-6,9,16-trione(Covalent)

88T.7: 6 residues within 4Å: Chain C: T.60, Y.62, F.70, C.71, I.72 Ligands: GD.8 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Y.62 88T.9: 4 residues within 4Å: Chain D: T.60, Y.62, C.71 Ligands: GD.10 No protein-ligand interaction detected (PLIP)

2 x GD: GADOLINIUM ATOM(Non-functional Binders)

GD.8: 1 residues within 4Å: Ligands: 88T.7 No protein-ligand interaction detected (PLIP) GD.10: 1 residues within 4Å: Ligands: 88T.9 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Galazzo, L. et al., The ABC transporter MsbA adopts the wide inward-open conformation in E. coli cells. Sci Adv (2022)

Release Date

2022-08-24

Peptides

ATP-dependent lipid A-core flippase: AB
Nanobody Nb_MsbA#1: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Membrane

We predict this structure to be a membrane protein.
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ATP-dependent lipid A-core flippase

Nanobody Nb_MsbA#1

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