SMTL ID : 8dmm.1

Structure of the vanadate-trapped MsbA bound to KDL

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

2 x AOV: ADP ORTHOVANADATE

AOV.1: 21 residues within 4Å: Chain A: D.118, Y.352, R.355, S.379, G.380, S.381, G.382, K.383, S.384, T.385, Y.394, Q.425, E.507, H.538 Chain B: V.480, L.481, S.483, G.484, G.485, Q.486, A.511 17 PLIP interactions: 13 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:D.118, A:D.118, A:G.380, A:G.380, A:S.381, A:K.383, A:S.384, A:S.384, A:T.385, A:Q.425, A:E.507, B:S.483, B:G.485, B:Q.486, B:Q.486 pi-Stacking: A:Y.352, A:Y.352 AOV.3: 21 residues within 4Å: Chain A: V.480, L.481, S.483, G.484, G.485, Q.486, A.511 Chain B: D.118, Y.352, R.355, S.379, G.380, S.381, G.382, K.383, S.384, T.385, Y.394, Q.425, E.507, H.538 17 PLIP interactions: 13 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:D.118, B:D.118, B:G.380, B:G.380, B:S.381, B:K.383, B:S.384, B:S.384, B:T.385, B:Q.425, B:E.507, A:S.483, A:G.485, A:Q.486, A:Q.486 pi-Stacking: B:Y.352, B:Y.352

2 x KDL: (2~{R},4~{R},5~{R},6~{R})-6-[(1~{R})-1,2-bis(oxidanyl)ethyl]-2-[(2~{R},4~{R},5~{R},6~{R})-6-[(1~{R})-1,2-bis(oxidanyl)ethyl]-2-carboxy-2-[[(2~{R},3~{S},4~{R},5~{R},6~{R})-5-[[(3~{R})-3-dodecanoyloxytetradecanoyl]amino]-6-[[(2~{R},3~{S},4~{R},5~{R},6~{R})-3-oxidanyl-5-[[(3~{R})-3-oxidanyltetradecanoyl]amino]-4-[(3~{R})-3-oxidanyltetradecanoyl]oxy-6-phosphonooxy-oxan-2-yl]methoxy]-3-phosphonooxy-4-[(3~{R})-3-tetradecanoyloxytetradecanoyl]oxy-oxan-2-yl]methoxy]-5-oxidanyl-oxan-4-yl]oxy-4,5-bis(oxidanyl)oxane-2-carboxylic acid(Non-covalent)

KDL.2: 18 residues within 4Å: Chain A: A.182, V.185, R.189, N.236, R.237, R.239, L.240, Q.241, K.244, I.251, P.254, I.255, L.258 Chain B: V.30, V.33, I.81, Y.84, Y.88 27 PLIP interactions: 17 interactions with chain A, 10 interactions with chain B Hydrophobic interactions: A:A.182, A:V.185, A:I.251, A:P.254, A:I.255, A:L.258, B:V.30, B:V.33, B:I.81, B:Y.84, B:Y.84, B:Y.88, B:Y.88 Hydrogen bonds: A:R.189, A:R.189, A:N.236, A:R.237, A:Q.241, A:K.244, B:Y.84, B:Y.88, B:Y.88 Salt bridges: A:R.189, A:R.189, A:R.239, A:K.244, A:K.244 KDL.4: 19 residues within 4Å: Chain A: V.30, V.33, I.81, Y.84, Y.88, W.92 Chain B: A.182, V.185, R.189, N.236, R.237, R.239, L.240, Q.241, K.244, I.251, P.254, I.255, L.258 25 PLIP interactions: 8 interactions with chain A, 17 interactions with chain B Hydrophobic interactions: A:V.33, A:I.81, A:Y.84, A:Y.88, A:Y.88, B:A.182, B:V.185, B:I.251, B:P.254, B:I.255, B:L.258 Hydrogen bonds: A:Y.84, A:Y.88, A:Y.88, B:R.189, B:R.189, B:N.236, B:R.237, B:Q.241, B:K.244 Salt bridges: B:R.189, B:R.189, B:R.239, B:K.244, B:K.244

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lyu, J. et al., Structural basis for lipid and copper regulation of the ABC transporter MsbA. Nat Commun (2022)

Release Date

2022-12-14

Peptides

ATP-binding transport protein MsbA: 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-binding transport protein MsbA

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