SMTL ID : 2qx0.1

Crystal Structure of Yersinia pestis HPPK (Ternary Complex)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.96, D.98 Ligands: MG.2, APC.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.96, A:D.98, H2O.1, H2O.1 MG.2: 6 residues within 4Å: Chain A: D.96, D.98, R.122 Ligands: MG.1, APC.3, PH2.4 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.96, A:D.98, H2O.1 MG.5: 4 residues within 4Å: Chain B: D.96, D.98 Ligands: MG.6, APC.7 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.96, B:D.98, H2O.10, H2O.10 MG.6: 6 residues within 4Å: Chain B: D.96, D.98, R.122 Ligands: MG.5, APC.7, PH2.8 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.96, B:D.98, H2O.10

2 x APC: DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER(Non-covalent)

APC.3: 20 residues within 4Å: Chain A: L.71, Q.75, R.93, D.96, L.97, D.98, I.99, R.111, L.112, T.113, I.114, H.116, Y.117, R.122 Chain B: R.89, Y.117 Ligands: MG.1, MG.2, PH2.4, APC.7 17 PLIP interactions: 14 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:Q.75, A:R.93, A:R.93, A:I.99, A:T.113, A:T.113, A:Y.117, B:R.89, B:Y.117 Water bridges: A:Q.75, A:R.89, A:R.89, A:R.111, A:R.122, B:R.89 Salt bridges: A:H.116, A:R.122 APC.7: 20 residues within 4Å: Chain A: R.89, Y.117 Chain B: L.71, Q.75, R.93, D.96, L.97, D.98, I.99, R.111, L.112, T.113, I.114, H.116, Y.117, R.122 Ligands: APC.3, MG.5, MG.6, PH2.8 19 PLIP interactions: 15 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:Q.75, B:R.93, B:R.93, B:I.99, B:T.113, B:T.113, B:Y.117, A:R.89, A:Y.117 Water bridges: B:Q.75, B:R.89, B:R.89, B:R.93, B:R.111, B:R.122, A:R.89, A:R.122 Salt bridges: B:H.116, B:R.122

2 x PH2: 2-AMINO-6-HYDROXYMETHYL-7,8-DIHYDRO-3H-PTERIDIN-4-ONE(Non-covalent)

PH2.4: 10 residues within 4Å: Chain A: T.43, K.44, P.45, L.46, F.54, N.56, D.96, F.124 Ligands: MG.2, APC.3 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:T.43, A:K.44, A:L.46, A:N.56, A:N.56 Water bridges: A:R.93, A:R.93, A:R.122, A:R.122 pi-Stacking: A:F.54, A:F.54, A:F.124 pi-Cation interactions: A:R.122, A:F.124 PH2.8: 10 residues within 4Å: Chain B: T.43, K.44, P.45, L.46, F.54, N.56, D.96, F.124 Ligands: MG.6, APC.7 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:T.43, B:K.44, B:L.46, B:N.56, B:N.56 Water bridges: B:R.93, B:R.93, B:R.122, B:R.122 pi-Stacking: B:F.54, B:F.54, B:F.124 pi-Cation interactions: B:R.122, B:F.124

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Blaszczyk, J. et al., Structure and activity of Yersinia pestis 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase as a novel target for the development of antiplague therapeutics. Acta Crystallogr.,Sect.D (2007)

Release Date

2007-10-23

Peptides

7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase