SMTL ID : 4nir.3 (2 other biounits)

Crystal structure of B. anthracis DHPS with compound 6: 3-[6-(trifluoromethyl)-1H-benzimidazol-2-yl]propan-1-ol

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.77 Å

Oligo State

homo-tetramer

Ligands

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

SO4.1: 6 residues within 4Å: Chain A: I.45, N.47, R.88, P.89, R.274, H.276 Ligand excluded by PLIP SO4.2: 2 residues within 4Å: Chain A: K.70, R.73 Ligand excluded by PLIP SO4.3: 2 residues within 4Å: Chain A: S.241, R.254 Ligand excluded by PLIP SO4.4: 1 residues within 4Å: Chain A: R.239 Ligand excluded by PLIP SO4.5: 3 residues within 4Å: Chain A: S.95, V.96, E.97 Ligand excluded by PLIP SO4.6: 4 residues within 4Å: Chain A: E.153, V.154, H.157, Y.158 Ligand excluded by PLIP SO4.9: 6 residues within 4Å: Chain B: I.45, N.47, R.88, P.89, R.274, H.276 Ligand excluded by PLIP SO4.10: 2 residues within 4Å: Chain B: K.70, R.73 Ligand excluded by PLIP SO4.11: 2 residues within 4Å: Chain B: S.241, R.254 Ligand excluded by PLIP SO4.12: 1 residues within 4Å: Chain B: R.239 Ligand excluded by PLIP SO4.13: 3 residues within 4Å: Chain B: S.95, V.96, E.97 Ligand excluded by PLIP SO4.14: 4 residues within 4Å: Chain B: E.153, V.154, H.157, Y.158 Ligand excluded by PLIP SO4.17: 3 residues within 4Å: Chain C: S.86, R.274, H.276 Ligand excluded by PLIP SO4.18: 3 residues within 4Å: Chain C: K.70, R.73, E.113 Ligand excluded by PLIP SO4.19: 2 residues within 4Å: Chain C: S.241, R.254 Ligand excluded by PLIP SO4.20: 1 residues within 4Å: Chain C: R.239 Ligand excluded by PLIP SO4.21: 2 residues within 4Å: Chain C: R.283 Chain D: L.249 Ligand excluded by PLIP SO4.23: 3 residues within 4Å: Chain D: S.86, R.274, H.276 Ligand excluded by PLIP SO4.24: 3 residues within 4Å: Chain D: K.70, R.73, E.113 Ligand excluded by PLIP SO4.25: 2 residues within 4Å: Chain D: S.241, R.254 Ligand excluded by PLIP SO4.26: 1 residues within 4Å: Chain D: R.239 Ligand excluded by PLIP SO4.27: 2 residues within 4Å: Chain C: L.249 Chain D: R.283 Ligand excluded by PLIP

6 x 6DH: 3-[6-(trifluoromethyl)-1H-benzimidazol-2-yl]propan-1-ol(Non-covalent)

6DH.7: 6 residues within 4Å: Chain A: W.143, K.146, A.147, R.168, D.169, N.170 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:W.143, A:W.143, A:A.147, A:D.169 Hydrogen bonds: A:D.169, A:N.170 Water bridges: A:R.168 6DH.8: 7 residues within 4Å: Chain A: L.255, E.256, E.280 Chain B: L.255, E.256, M.284 Ligands: 6DH.16 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:L.255, A:L.255, A:E.256, B:L.255 Hydrogen bonds: A:E.280, A:E.280, B:E.256 6DH.15: 6 residues within 4Å: Chain B: W.143, K.146, A.147, R.168, D.169, N.170 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:W.143, B:W.143, B:A.147, B:D.169 Hydrogen bonds: B:D.169, B:N.170 Water bridges: B:R.168 6DH.16: 7 residues within 4Å: Chain A: L.255, E.256, M.284 Chain B: L.255, E.256, E.280 Ligands: 6DH.8 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:L.255, B:L.255, B:E.256, A:L.255 Hydrogen bonds: B:E.280, B:E.280, A:E.256 6DH.22: 8 residues within 4Å: Chain C: L.255, E.256, E.280, M.281 Chain D: L.255, E.256, E.280 Ligands: 6DH.28 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:L.255, C:E.256, D:E.280 Hydrogen bonds: C:K.279, C:E.280, D:E.256 6DH.28: 8 residues within 4Å: Chain C: L.255, E.256, E.280 Chain D: L.255, E.256, E.280, M.281 Ligands: 6DH.22 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:L.255, D:E.256, C:E.280 Hydrogen bonds: D:K.279, D:E.280, C:E.256

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hammoudeh, D.I. et al., Identification and characterization of an allosteric inhibitory site on dihydropteroate synthase. Acs Chem.Biol. (2014)

Release Date

2014-05-14

Peptides

Dihydropteroate Synthase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
B

D
B

Dihydropteroate Synthase

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