SMTL ID : 6ull.1

BshB from Bacillus subtilis complexed with a substrate analogue

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

homo-hexamer

Ligands

6 x RWI: (2S)-2-({2-deoxy-2-[(hydroxycarbamoyl)amino]-alpha-D-glucopyranosyl}oxy)butanedioic acid(Non-covalent)

RWI.1: 22 residues within 4Å: Chain A: H.32, D.34, D.35, I.38, A.62, L.64, S.65, S.66, R.73, D.96, R.97, R.129, H.130, D.132, H.133, I.171, T.210, P.211, L.212 Chain C: F.145, I.149 Ligands: ZN.2 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:D.34, A:A.62, A:S.66, A:R.73, A:R.73 Water bridges: A:D.34, A:D.34, A:N.67, A:R.129, A:N.172 Salt bridges: A:R.129, A:H.130 RWI.4: 22 residues within 4Å: Chain A: F.145, I.149 Chain B: H.32, D.34, D.35, I.38, A.62, L.64, S.65, S.66, R.73, D.96, R.97, R.129, H.130, D.132, H.133, I.171, T.210, P.211, L.212 Ligands: ZN.5 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:D.34, B:A.62, B:S.66, B:R.73, B:R.73 Water bridges: B:D.34, B:D.34, B:N.67, B:R.129, B:N.172 Salt bridges: B:R.129, B:H.130 RWI.7: 22 residues within 4Å: Chain B: F.145, I.149 Chain C: H.32, D.34, D.35, I.38, A.62, L.64, S.65, S.66, R.73, D.96, R.97, R.129, H.130, D.132, H.133, I.171, T.210, P.211, L.212 Ligands: ZN.8 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:D.34, C:A.62, C:S.66, C:R.73, C:R.73 Water bridges: C:D.34, C:D.34, C:N.67, C:R.129, C:N.172 Salt bridges: C:R.129, C:H.130 RWI.10: 22 residues within 4Å: Chain D: H.32, D.34, D.35, I.38, A.62, L.64, S.65, S.66, R.73, D.96, R.97, R.129, H.130, D.132, H.133, I.171, T.210, P.211, L.212 Chain F: F.145, I.149 Ligands: ZN.11 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:D.34, D:A.62, D:S.66, D:R.73, D:R.73 Water bridges: D:D.34, D:D.34, D:N.67, D:R.129, D:N.172 Salt bridges: D:R.129, D:H.130 RWI.13: 22 residues within 4Å: Chain D: F.145, I.149 Chain E: H.32, D.34, D.35, I.38, A.62, L.64, S.65, S.66, R.73, D.96, R.97, R.129, H.130, D.132, H.133, I.171, T.210, P.211, L.212 Ligands: ZN.14 12 PLIP interactions: 12 interactions with chain E Hydrogen bonds: E:D.34, E:A.62, E:S.66, E:R.73, E:R.73 Water bridges: E:D.34, E:D.34, E:N.67, E:R.129, E:N.172 Salt bridges: E:R.129, E:H.130 RWI.16: 22 residues within 4Å: Chain E: F.145, I.149 Chain F: H.32, D.34, D.35, I.38, A.62, L.64, S.65, S.66, R.73, D.96, R.97, R.129, H.130, D.132, H.133, I.171, T.210, P.211, L.212 Ligands: ZN.17 12 PLIP interactions: 12 interactions with chain F Hydrogen bonds: F:D.34, F:A.62, F:S.66, F:R.73, F:R.73 Water bridges: F:D.34, F:D.34, F:N.67, F:R.129, F:N.172 Salt bridges: F:R.129, F:H.130

6 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: H.32, D.35, H.133 Ligands: RWI.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.32, A:D.35, A:D.35, A:H.133 ZN.5: 4 residues within 4Å: Chain B: H.32, D.35, H.133 Ligands: RWI.4 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.32, B:D.35, B:D.35, B:H.133 ZN.8: 4 residues within 4Å: Chain C: H.32, D.35, H.133 Ligands: RWI.7 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.32, C:D.35, C:D.35, C:H.133 ZN.11: 4 residues within 4Å: Chain D: H.32, D.35, H.133 Ligands: RWI.10 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.32, D:D.35, D:D.35, D:H.133 ZN.14: 4 residues within 4Å: Chain E: H.32, D.35, H.133 Ligands: RWI.13 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:H.32, E:D.35, E:D.35, E:H.133 ZN.17: 4 residues within 4Å: Chain F: H.32, D.35, H.133 Ligands: RWI.16 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:H.32, F:D.35, F:D.35, F:H.133

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 2 residues within 4Å: Chain A: V.208, S.209 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.209 SO4.6: 2 residues within 4Å: Chain B: V.208, S.209 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.209 SO4.9: 2 residues within 4Å: Chain C: V.208, S.209 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.209 SO4.12: 2 residues within 4Å: Chain D: V.208, S.209 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:S.209 SO4.15: 2 residues within 4Å: Chain E: V.208, S.209 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:S.209 SO4.18: 2 residues within 4Å: Chain F: V.208, S.209 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:S.209

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Woodward, R.L. et al., X-ray crystallographic structure of BshB, the zinc-dependent deacetylase involved in bacillithiol biosynthesis. Protein Sci. (2020)

Release Date

2020-01-08

Peptides

N-acetyl-alpha-D-glucosaminyl L-malate deacetylase 1: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

N-acetyl-alpha-D-glucosaminyl L-malate deacetylase 1

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