SMTL ID : 4ewl.1 (1 other biounit)

Crystal Structure of MshB with glycerol and Acetate bound in the active site

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

2 x PE4: 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL(Non-functional Binders)

PE4.1: 10 residues within 4Å: Chain A: G.66, Y.67, G.70, E.71 Chain B: G.66, Y.67, G.70, E.71, R.77 Ligands: PE4.15 8 PLIP interactions: 4 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:G.70, B:R.77, B:R.77, A:G.70 Water bridges: B:A.74, A:A.74, A:R.77, A:R.77 PE4.15: 15 residues within 4Å: Chain A: R.52, W.53 Chain B: T.73, R.77, S.82, A.83, P.84, I.85, Y.86, G.88, G.89, A.90, G.119, A.120 Ligands: PE4.1 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:R.77, B:S.82, B:Y.86, A:R.52 Water bridges: B:A.90, B:A.90, A:R.52, A:Y.67

9 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 8 residues within 4Å: Chain A: T.29, A.33, Q.34, V.35, H.36, G.80, V.81, S.82 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:A.33, A:V.35, A:S.82, A:S.82 Water bridges: A:A.83 GOL.5: 9 residues within 4Å: Chain A: H.13, G.43, E.45, G.46, R.68, D.95, G.97, M.98, H.144 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.68, A:R.68, A:G.97, A:Y.142 GOL.6: 5 residues within 4Å: Chain A: V.158, V.177, P.178, G.277, G.278 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.278 GOL.7: 6 residues within 4Å: Chain A: D.291, A.294, G.295, L.296, G.297, T.299 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.291, A:D.291, A:G.295, A:G.297 Water bridges: A:F.298, A:T.299 GOL.10: 8 residues within 4Å: Chain B: H.13, G.43, G.46, R.68, D.95, G.97, M.98, H.144 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:G.43, B:R.68, B:R.68, B:D.95, B:G.97 Water bridges: B:M.98 GOL.11: 8 residues within 4Å: Chain B: T.29, A.33, Q.34, V.35, H.36, G.80, V.81, S.82 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:A.33, B:V.35, B:H.36, B:G.80, B:S.82 Water bridges: B:A.83 GOL.12: 5 residues within 4Å: Chain B: V.158, V.177, P.178, G.277, G.278 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.177, B:G.278 Water bridges: B:G.278 GOL.13: 5 residues within 4Å: Chain B: A.282, A.294, G.295, G.297, F.298 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:A.282, B:G.295, B:G.297 Water bridges: B:D.291, B:L.296, B:F.298 GOL.14: 3 residues within 4Å: Chain B: S.188, D.220, R.286 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.188, B:S.188, B:R.286

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: H.13, D.16, H.147 Ligands: ACT.4 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:H.13, A:D.16, A:D.16, A:H.147, ACT.4 ZN.8: 4 residues within 4Å: Chain B: H.13, D.16, H.147 Ligands: ACT.9 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:H.13, B:D.16, B:D.16, B:H.147, ACT.9

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.4: 7 residues within 4Å: Chain A: H.13, D.15, D.16, L.19, Y.142, H.147 Ligands: ZN.3 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.19 Hydrogen bonds: A:D.15, A:Y.142 Salt bridges: A:H.13, A:H.147 ACT.9: 6 residues within 4Å: Chain B: H.13, D.15, D.16, Y.142, H.147 Ligands: ZN.8 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.15, B:Y.142 Salt bridges: B:H.13, B:H.147

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Broadley, S.G. et al., A new crystal form of MshB from Mycobacterium tuberculosis with glycerol and acetate in the active site suggests the catalytic mechanism. Acta Crystallogr.,Sect.D (2012)

Release Date

2012-09-26

Peptides

1D-myo-inositol 2-acetamido-2-deoxy-alpha-D-glucopyranoside deacetylase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

1D-myo-inositol 2-acetamido-2-deoxy-alpha-D-glucopyranoside deacetylase

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