SMTL ID : 7bvh.1

Crystal structure of arabinosyltransferase EmbC2-AcpM2 complex from Mycobacterium smegmatis complexed with di-arabinose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.30 Å

Oligo State

hetero-2-2-mer

Ligands

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

BXY-BXY.1: 13 residues within 4Å: Chain A: D.292, Y.295, N.311, W.315, E.320, Y.327, W.585, H.587, W.640, W.978, V.1017 Ligands: BGC-GLC.2, PO4.10 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.311, A:E.320, A:Y.327 BXY-BXY.6: 13 residues within 4Å: Chain B: D.292, Y.295, I.296, M.299, N.311, W.315, E.320, Y.327, W.585, W.978, V.1017 Ligands: BGC-GLC.7, PO4.14 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.292, B:N.311, B:E.320, B:E.320, B:Y.327

6 x BGC- GLC: alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose(Non-covalent)

BGC-GLC.2: 11 residues within 4Å: Chain A: W.315, E.320, F.323, P.439, S.499, K.502, S.503, P.507, S.508, P.582 Ligands: BXY-BXY.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.499, A:P.507, A:E.320, A:P.507 BGC-GLC.3: 4 residues within 4Å: Chain A: W.511, F.512 Chain B: T.662 Ligands: BXY.16 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.511 BGC-GLC.4: 5 residues within 4Å: Chain A: T.661, T.662 Chain B: W.511, F.512 Ligands: BXY.12 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.655, A:T.662 BGC-GLC.5: 4 residues within 4Å: Chain A: P.648, W.649, S.652, F.656 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.656, A:V.647, A:W.649, A:S.652 BGC-GLC.7: 13 residues within 4Å: Chain B: W.315, E.320, S.321, F.323, P.439, S.499, K.502, S.503, P.507, S.508, P.582 Ligands: BXY-BXY.6, PO4.14 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.499, B:S.499, B:K.502, B:S.508, B:E.320, B:P.507 BGC-GLC.8: 4 residues within 4Å: Chain B: P.648, W.649, S.652, L.719 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:W.649, B:S.652, B:S.652

2 x CA: CALCIUM ION(Non-covalent)

CA.9: 5 residues within 4Å: Chain A: S.848, D.942, D.944, H.949, W.950 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.942, A:D.942, A:D.944, A:H.949 CA.13: 5 residues within 4Å: Chain B: Q.854, D.942, D.944, A.946, H.949 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.942, B:D.942, B:D.944

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

PO4.10: 8 residues within 4Å: Chain A: D.292, R.396, T.583, W.585, H.587, H.588 Ligands: BXY-BXY.1, BXY-BXY.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.583, A:T.583, A:H.587 Salt bridges: A:R.396, A:H.588 PO4.14: 9 residues within 4Å: Chain B: D.292, R.396, T.583, W.585, H.587, H.588 Ligands: BXY-BXY.6, BXY-BXY.6, BGC-GLC.7 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.292, B:D.292, B:T.583, B:W.585 Salt bridges: B:R.396, B:H.588

4 x BXY: alpha-D-arabinofuranose(Non-covalent)

BXY.11: 7 residues within 4Å: Chain A: R.552, K.553, A.611, M.612, K.613, S.614, N.617 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.552, A:K.613, A:S.614, A:N.617 Salt bridges: A:K.553 BXY.12: 4 residues within 4Å: Chain A: F.658, T.662 Ligands: BGC-GLC.4, BGC-GLC.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.662 BXY.15: 6 residues within 4Å: Chain B: K.553, A.611, M.612, K.613, S.614, N.617 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:A.611, B:K.613, B:S.614, B:N.617 Salt bridges: B:K.553 BXY.16: 4 residues within 4Å: Chain B: F.658, T.662 Ligands: BGC-GLC.3, BGC-GLC.3 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.662, B:T.662

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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