SMTL ID : 8i8r.1

Cryo-EM Structure of OmpC3-MlaA Complex in MSP2N2 Nanodiscs

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-1-mer

Ligands

3 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.1: 18 residues within 4Å: Chain A: F.88, Y.90, A.129, Y.131, V.147, Y.149, K.152, D.178, V.180, K.201, D.204, R.217 Chain C: H.21, F.23, K.27, D.30, L.340, G.341 21 PLIP interactions: 15 interactions with chain A, 6 interactions with chain C Hydrophobic interactions: A:F.88, A:F.88, A:Y.90, A:Y.131, A:V.147, A:V.147, A:Y.149, A:V.180, A:V.180, A:V.180, C:F.23, C:F.23, C:L.340 Hydrogen bonds: A:K.152, A:D.204, C:D.30, C:D.30 Salt bridges: A:K.201, A:R.217, A:R.217, C:K.27 KDL.2: 21 residues within 4Å: Chain A: H.21, F.23, S.24, K.27, V.338, L.340 Chain B: F.88, Y.90, A.129, T.130, Y.131, V.147, Q.148, Y.149, K.152, D.178, V.180, K.201, R.217 Chain D: I.91, M.94 27 PLIP interactions: 16 interactions with chain B, 9 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: B:F.88, B:Y.90, B:Y.90, B:Y.131, B:V.147, B:V.147, B:Y.149, B:Y.149, B:Y.149, B:V.180, B:V.180, B:V.180, A:H.21, A:F.23, A:F.23, A:F.23, A:F.23, A:V.338, A:L.340, D:I.91, D:I.91 Hydrogen bonds: B:K.152, B:D.178 Salt bridges: B:K.201, B:R.217, A:K.27, A:K.27 KDL.3: 16 residues within 4Å: Chain B: H.21, F.23, S.24, K.27, V.338, L.340 Chain C: F.88, Y.90, A.129, Y.131, Y.149, K.152, D.178, V.180, K.201, R.217 16 PLIP interactions: 11 interactions with chain C, 5 interactions with chain B Hydrophobic interactions: C:F.88, C:Y.90, C:Y.131, C:Y.149, C:Y.149, C:V.180, C:V.180, B:F.23, B:F.23, B:V.338 Hydrogen bonds: C:K.152, C:D.178 Salt bridges: C:K.201, C:R.217, B:K.27, B:K.27

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yeow, J. et al., Molecular mechanism of phospholipid transport at the bacterial outer membrane interface. Nat Commun (2023)

Release Date

2023-12-20

Peptides

Outer membrane porin C: ABC
Intermembrane phospholipid transport system lipoprotein MlaA: D

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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Outer membrane porin C

Intermembrane phospholipid transport system lipoprotein MlaA

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