SMTL ID : 7bve.1

Cryo-EM structure of Mycobacterium smegmatis arabinosyltransferase EmbC2-AcpM2 in complex with ethambutol

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-mer

Ligands

2 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: D.929, D.931, A.933, H.936 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.929 CA.4: 4 residues within 4Å: Chain B: D.929, D.931, A.933, H.936 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.929, B:D.931

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

PO4.2: 4 residues within 4Å: Chain A: R.383, T.570, H.575 Ligands: 95E.3 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.383, A:H.575 PO4.5: 4 residues within 4Å: Chain B: R.383, T.570, H.575 Ligands: 95E.6 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.383, B:H.575

2 x 95E: Ethambutol(Non-covalent)

95E.3: 9 residues within 4Å: Chain A: D.279, Y.282, I.283, Y.314, R.383, W.572, W.965, V.1004 Ligands: PO4.2 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.282, A:I.283, A:W.965, A:V.1004 Hydrogen bonds: A:N.298 95E.6: 9 residues within 4Å: Chain B: D.279, Y.282, I.283, Y.314, R.383, W.572, W.965, V.1004 Ligands: PO4.5 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:Y.282, B:I.283, B:W.965, B:V.1004 Hydrogen bonds: B:N.298

2 x PN7: N~3~-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-N-(2-sulfanylethyl)-beta-alaninamide(Covalent)

PN7.7: 12 residues within 4Å: Chain A: H.235, R.244, H.245, K.246, R.247, F.248, S.251, R.401, T.405 Chain C: S.41, L.42, V.45 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: C:L.42, C:V.45, A:T.405 Hydrogen bonds: A:R.247 Salt bridges: A:R.247 PN7.8: 12 residues within 4Å: Chain B: H.235, R.244, H.245, K.246, R.247, F.248, S.251, R.401, T.405 Chain D: S.41, L.42, V.45 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain D Hydrophobic interactions: B:T.405, D:L.42, D:V.45 Hydrogen bonds: B:R.247 Salt bridges: B:R.247

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 EmbC: AB
Meromycolate extension acyl carrier protein: 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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Integral membrane indolylacetylinositol arabinosyltransferase EmbC

Meromycolate extension acyl carrier protein

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