SMTL ID : 7bvg.1

Cryo-EM structure of Mycobacterium smegmatis arabinosyltransferase EmbA-EmbB-AcpM2 in complex with di-arabinose.

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

1 x BXY- BXY: alpha-D-arabinofuranose-(1-5)-alpha-D-arabinofuranose(Non-covalent)

BXY-BXY.1: 11 residues within 4Å: Chain B: D.285, Y.288, N.304, E.313, Y.320, R.389, R.495, H.580, W.972, W.1012 Ligands: PO4.5 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.304, B:E.313, B:R.389, B:R.495

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: 16 residues within 4Å: Chain A: D.269, Y.272, N.273, E.297, F.300, R.373, P.374, P.416, Q.417, K.479, Y.480, L.558, P.560, T.561, W.563, Q.566 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.300, A:F.300, A:K.479, A:Y.480, A:L.558, A:P.560 Hydrogen bonds: A:E.297, A:Q.417, A:Q.566 Salt bridges: A:R.373, A:R.373

2 x CDL: CARDIOLIPIN(Non-covalent)

CDL.3: 17 residues within 4Å: Chain A: F.522, M.526, R.530, R.594, F.605, G.651, L.652, H.658 Chain B: L.442, A.443, R.446, F.537, W.558, G.562, F.565, F.569, F.570 13 PLIP interactions: 8 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:L.442, B:F.537, B:W.558, B:W.558, B:F.565, B:F.569, B:F.570, A:F.522, A:F.605, A:L.652 Hydrogen bonds: B:R.446 Salt bridges: A:R.530, A:H.658 CDL.7: 21 residues within 4Å: Chain A: L.426, R.430, Y.495, F.522, I.525, W.543, G.547, I.551, L.554, L.555, W.609 Chain B: R.545, R.609, N.610, S.616, S.662, A.666, L.667, A.669, F.670, H.673 17 PLIP interactions: 10 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:L.426, A:L.426, A:F.522, A:F.522, A:I.525, A:I.551, A:L.554, A:L.555, A:W.609, B:R.609, B:A.666, B:L.667 Salt bridges: A:R.430, B:R.545, B:R.609, B:R.609, B:H.673

2 x CA: CALCIUM ION(Non-covalent)

CA.4: 3 residues within 4Å: Chain A: D.939, N.941, Q.946 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.939, A:Q.946 CA.8: 4 residues within 4Å: Chain B: D.936, S.938, S.940, D.943 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.936

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

PO4.5: 7 residues within 4Å: Chain B: R.389, Q.431, T.576, W.578, H.581 Ligands: BXY-BXY.1, BXY-BXY.1 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.576 Salt bridges: B:R.389, B:H.581

1 x PNS: 4'-PHOSPHOPANTETHEINE(Covalent)

PNS.6: 8 residues within 4Å: Chain B: M.251, H.252, R.253, L.254, P.256, T.257, W.259 Chain C: S.41 9 PLIP interactions: 2 interactions with chain C, 7 interactions with chain B Hydrogen bonds: C:S.41, C:S.41, B:H.252, B:R.253, B:T.257, B:T.257 Hydrophobic interactions: B:H.252, B:R.253 Salt bridges: B:R.253

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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