SMTL ID : 3ls6.1

Crystal structure of 3,4-Dihydroxy-2-butanone 4-phosphate synthase in complex with sulfate and zinc

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.86 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 7 residues within 4Å: Chain A: R.37, E.38, R.150, G.152, H.153, T.154 Ligands: ZN.2 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:H.153, A:T.154, A:T.154 Water bridges: A:T.154 Salt bridges: A:R.37, A:R.150 SO4.8: 8 residues within 4Å: Chain B: R.37, E.38, T.93, R.150, G.152, H.153, T.154 Ligands: ZN.10 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:H.153, B:T.154, B:T.154 Water bridges: B:T.154 Salt bridges: B:R.37, B:R.150 SO4.9: 5 residues within 4Å: Chain B: T.71, E.72, D.73, A.144 Ligands: ZN.11 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.72, B:D.73 Water bridges: B:A.144

11 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: E.38, D.42, H.153 Ligands: SO4.1, MG.6 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.38, A:H.153, H2O.1, H2O.1 ZN.3: 2 residues within 4Å: Chain A: H.136 Chain B: E.174 5 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: A:H.136, B:E.174, H2O.5, H2O.11, H2O.11 ZN.4: 2 residues within 4Å: Chain A: H.61, H.195 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.61, A:H.195, H2O.5, H2O.5, H2O.5 ZN.5: 1 residues within 4Å: Chain A: D.130 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.130, H2O.4, H2O.4, H2O.4, H2O.4 ZN.10: 4 residues within 4Å: Chain B: E.38, D.42, H.153 Ligands: SO4.8 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.38, B:H.153, H2O.7, H2O.13 ZN.11: 3 residues within 4Å: Chain B: D.73, K.76 Ligands: SO4.9 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.73, B:D.73 ZN.12: 1 residues within 4Å: Chain B: H.195 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.195, H2O.11, H2O.11 ZN.13: 2 residues within 4Å: Chain B: H.61 Ligands: ZN.15 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.61, H2O.11, H2O.13 ZN.14: 3 residues within 4Å: Chain A: E.174 Chain B: H.136 Ligands: MG.6 5 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: B:H.136, A:E.174, H2O.5, H2O.5, H2O.11 ZN.15: 4 residues within 4Å: Chain B: L.57, H.61, H.195 Ligands: ZN.13 No protein-ligand interaction detected (PLIP) ZN.16: 1 residues within 4Å: Chain B: H.212 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.212, H2O.11

1 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 5 residues within 4Å: Chain A: E.38, E.40 Chain B: H.136 Ligands: ZN.2, ZN.14 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.38, H2O.5, H2O.5, H2O.11, H2O.11

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 6 residues within 4Å: Chain A: R.60, H.61, L.175, T.176, N.177, D.178 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.60, A:R.60, A:T.176, A:N.177 Water bridges: A:D.178, A:D.178

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kumar, P. et al., Potential anti-bacterial drug target: structural characterization of 3,4-dihydroxy-2-butanone-4-phosphate synthase from Salmonella typhimurium LT2. Proteins (2010)

Release Date

2010-09-15

Peptides

3,4-Dihydroxy-2-butanone 4-phosphate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

3,4-Dihydroxy-2-butanone 4-phosphate synthase

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