SMTL ID : 3tyz.1

Crystal Structure of the Yersinia pestis Dihydropteroate synthetase with substrate transition state complex.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.07 Å

Oligo State

homo-dimer

Ligands

2 x XHP: 2-amino-6-methylidene-6,7-dihydropteridin-4(3H)-one(Non-covalent)

XHP.1: 13 residues within 4Å: Chain A: T.65, D.99, N.118, I.120, M.142, D.188, F.193, L.218, G.220, K.224, R.258 Ligands: POP.2, PAB.3 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.118, A:N.118, A:K.224 Water bridges: A:G.220, A:G.220 Salt bridges: A:D.99, A:D.188 pi-Cation interactions: A:R.258 XHP.5: 12 residues within 4Å: Chain B: D.99, N.118, I.120, M.142, D.188, F.193, L.218, G.220, K.224, R.258 Ligands: POP.6, PAB.7 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:F.193 Hydrogen bonds: B:N.118, B:N.118, B:K.224 Water bridges: B:T.65, B:G.190, B:F.191 Salt bridges: B:D.99, B:D.188 pi-Cation interactions: B:R.258

2 x POP: PYROPHOSPHATE 2-(Non-covalent)

POP.2: 12 residues within 4Å: Chain A: I.23, N.25, S.30, F.31, S.64, T.65, R.66, R.258, H.260 Ligands: XHP.1, PAB.3, MG.4 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:N.25, A:N.25, A:F.31, A:S.64, A:T.65, A:T.65 Water bridges: A:S.30, A:S.222, A:R.258 Salt bridges: A:R.258, A:H.260 POP.6: 12 residues within 4Å: Chain B: I.23, N.25, S.30, F.31, S.64, T.65, R.66, R.258, H.260 Ligands: XHP.5, PAB.7, MG.8 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:N.25, B:N.25, B:F.31, B:T.65, B:R.66 Water bridges: B:S.32, B:D.99, B:R.258 Salt bridges: B:R.258, B:H.260

2 x PAB: 4-AMINOBENZOIC ACID(Non-covalent)

PAB.3: 11 residues within 4Å: Chain A: F.31, T.65, R.66, P.67, M.151, G.192, F.193, K.224, S.225 Ligands: XHP.1, POP.2 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.31, A:R.66, A:F.193, A:K.224 Hydrogen bonds: A:T.65, A:T.65, A:S.225 Water bridges: A:N.200, A:S.225, A:M.226 pi-Cation interactions: A:K.224 PAB.7: 11 residues within 4Å: Chain B: F.31, T.65, R.66, P.67, M.151, G.192, F.193, K.224, S.225 Ligands: XHP.5, POP.6 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:F.31, B:R.66, B:K.224 Hydrogen bonds: B:T.65, B:S.225 Water bridges: B:G.192, B:S.225, B:M.226 pi-Stacking: B:F.193 pi-Cation interactions: B:K.224

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 4 residues within 4Å: Chain A: N.25, S.30, R.258 Ligands: POP.2 No protein-ligand interaction detected (PLIP) MG.8: 4 residues within 4Å: Chain B: N.25, S.30, R.258 Ligands: POP.6 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yun, M.K. et al., Catalysis and sulfa drug resistance in dihydropteroate synthase. Science (2012)

Release Date

2012-03-14

Peptides

7,8-dihydropteroate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

7,8-dihydropteroate synthase

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