SMTL ID : 7bvc.1

Cryo-EM structure of Mycobacterium smegmatis arabinosyltransferase EmbA-EmbB-AcpM2 in complex with ethambutol

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

2 x CDL: CARDIOLIPIN(Non-covalent)

CDL.1: 18 residues within 4Å: Chain A: F.522, M.526, R.530, R.594, W.609, G.651, G.655, H.658 Chain B: A.443, E.507, Y.511, F.537, L.540, R.554, W.558, G.562, F.565, F.569 13 PLIP interactions: 6 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:F.522, A:W.609, B:E.507, B:Y.511, B:F.537, B:L.540, B:F.565 Salt bridges: A:R.530, A:R.594, A:H.658, A:H.658, B:R.554 Hydrogen bonds: B:R.446 CDL.7: 23 residues within 4Å: Chain A: L.426, V.427, R.430, Y.495, F.522, I.525, W.543, G.547, A.550, I.551, L.554, L.555 Chain B: R.545, R.609, N.610, A.613, S.616, F.620, F.659, S.662, L.667, F.670, H.673 15 PLIP interactions: 8 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:L.426, A:F.522, A:F.522, A:I.525, A:A.550, A:I.551, A:L.555, B:F.620, B:F.659, B:L.667 Salt bridges: A:R.430, B:R.545, B:R.609, B:R.609, B:H.673

1 x F8L: [(2Z,6E,10E,14Z,18E,22Z,26Z)-3,7,11,15,19,23,27,31,35,39-decamethyltetraconta-2,6,10,14,18,22,26,30,34,38-decaenyl] [(2S,3S,4S,5R)-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl] hydrogen phosphate(Non-covalent)

F8L.2: 17 residues within 4Å: Chain A: D.269, Y.272, N.273, F.300, Q.304, R.373, P.416, Q.417, V.456, V.476, K.479, Y.480, L.558, T.561, W.563, Q.566, N.788 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:F.300, A:P.416, A:V.456, A:K.479, A:Y.480, A:L.558 Hydrogen bonds: A:N.273, A:Q.304, A:R.373, A:T.561, A:T.561, A:Q.566, A:N.788 Salt bridges: A:R.373, A:R.373

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 4 residues within 4Å: Chain A: E.839, D.939, N.941, Q.946 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:N.941, A:Q.946 CA.8: 4 residues within 4Å: Chain B: D.936, S.938, S.940, D.943 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.936, B:S.938, B:D.943

1 x PNS: 4'-PHOSPHOPANTETHEINE(Non-covalent)

PNS.4: 10 residues within 4Å: Chain B: M.251, H.252, R.253, I.255, P.256, T.257, W.259, R.407 Chain C: S.41, L.42 8 PLIP interactions: 2 interactions with chain C, 6 interactions with chain B Hydrophobic interactions: C:L.42 Hydrogen bonds: C:S.41, B:H.252, B:T.257, B:T.257, B:R.407, B:R.407 Salt bridges: B:R.253

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.5: 6 residues within 4Å: Chain B: R.389, Q.431, T.576, W.578, H.581 Ligands: 95E.6 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:W.578 Salt bridges: B:R.389, B:H.581

1 x 95E: Ethambutol(Non-covalent)

95E.6: 11 residues within 4Å: Chain B: D.285, Y.288, I.289, N.304, E.313, Y.320, R.389, H.580, W.972, W.1012 Ligands: PO4.5 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:I.289, B:W.972, B:W.1012 Hydrogen bonds: B:N.304, B:E.313, B:H.580

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, L. et al., Structures of cell wall arabinosyltransferases with the anti-tuberculosis drug ethambutol. Science (2020)

Release Date

2020-04-29

Peptides

Integral membrane indolylacetylinositol arabinosyltransferase EmbA: A
Integral membrane indolylacetylinositol arabinosyltransferase EmbB: B
Meromycolate extension acyl carrier protein: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
P

Membrane

We predict this structure to be a membrane protein.
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Integral membrane indolylacetylinositol arabinosyltransferase EmbA

Integral membrane indolylacetylinositol arabinosyltransferase EmbB

Meromycolate extension acyl carrier protein

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