SMTL ID : 7ph3.1

AMP-PNP bound nanodisc reconstituted MsbA with nanobodies, spin-labeled at position A60C

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.80 Å

Oligo State

hetero-2-2-mer

Ligands

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

ANP.1: 23 residues within 4Å: Chain A: D.128, Y.362, R.365, 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, A.521 Ligands: MG.2 25 PLIP interactions: 7 interactions with chain B, 18 interactions with chain A Hydrogen bonds: B:S.493, B:S.493, B:G.494, B:G.495, B:Q.496, B:Q.496, B:A.521, A:D.128, A:D.128, A:G.390, A:G.390, A:S.391, A:G.392, A:K.393, A:K.393, A:K.393, A:S.394, A:S.394, A:S.394, A:T.395, A:Y.404, A:Q.435, A:Q.435 pi-Stacking: A:Y.362, A:Y.362 ANP.5: 22 residues within 4Å: Chain A: V.490, L.491, S.493, G.494, G.495, Q.496, A.521 Chain B: D.128, Y.362, R.365, S.389, G.390, S.391, G.392, K.393, S.394, T.395, Y.404, Q.435, E.517, H.548 Ligands: MG.6 25 PLIP interactions: 18 interactions with chain B, 7 interactions with chain A Hydrogen bonds: B:D.128, B:D.128, B:R.365, B:G.390, B:G.390, B:S.391, B:G.392, B:K.393, B:K.393, B:K.393, B:S.394, B:S.394, 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, A:A.521 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.6: 3 residues within 4Å: Chain B: S.394, Q.435 Ligands: ANP.5 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: 11 residues within 4Å: Chain A: W.21, F.24, R.25, L.27, W.28, I.31, L.38, S.104, V.107, S.150, L.154 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.24, A:L.27, A:W.28, A:L.38, A:V.107 Hydrogen bonds: A:R.25, A:R.25 LMT.8: 12 residues within 4Å: Chain B: W.21, F.24, R.25, L.27, W.28, I.31, L.38, V.103, S.104, V.107, S.150, L.154 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:F.24, B:F.24, B:L.27, B:W.28, B:L.38, B:V.103, B:V.107, B:L.154 Hydrogen bonds: B:R.25, B:R.25, B:R.25

2 x 3PE: 1,2-Distearoyl-sn-glycerophosphoethanolamine(Non-covalent)

3PE.4: 15 residues within 4Å: Chain A: I.188, I.191, V.196, K.254, S.257, A.258, I.261, P.264, I.265, L.268, I.269 Chain B: I.87, G.90, I.91, Y.94 13 PLIP interactions: 9 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:I.188, A:I.191, A:V.196, A:A.258, A:I.261, A:I.261, A:P.264, A:I.265, A:L.268, B:I.87, B:Y.94, B:Y.94, B:Y.94 3PE.7: 14 residues within 4Å: Chain A: I.87, G.90, I.91, Y.94 Chain B: I.188, V.196, K.254, S.257, A.258, I.261, P.264, I.265, L.268, I.269 12 PLIP interactions: 9 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:I.188, B:V.196, B:A.258, B:I.261, B:I.261, B:P.264, B:I.265, B:L.268, B:I.269, A:I.87, A:Y.94, A:Y.94

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.9: 4 residues within 4Å: Chain B: E.578 Chain C: E.49, C.63 Ligands: GD.10 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:E.49 88T.11: 5 residues within 4Å: Chain A: E.578 Chain D: R.41, E.49, C.63 Ligands: GD.12 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:E.49 Hydrogen bonds: D:R.41

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

GD.10: 1 residues within 4Å: Ligands: 88T.9 No protein-ligand interaction detected (PLIP) GD.12: 1 residues within 4Å: Ligands: 88T.11 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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