SMTL ID : 5etp.1

E. coli 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase complexed with AMPCPP and inhibitor at 1.05 angstrom resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.05 Å

Oligo State

monomer

Ligands

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

APC.1: 20 residues within 4Å: Chain A: L.74, Q.78, R.86, R.88, W.93, R.96, D.99, L.100, D.101, I.102, R.114, L.115, T.116, V.117, H.119, Y.120, R.125 Ligands: CA.4, CA.5, 5RZ.9 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:Q.78, A:R.86, A:R.86, A:R.88, A:R.88, A:R.96, A:R.96, A:D.99, A:I.102, A:T.116, A:T.116 Salt bridges: A:H.119, A:R.125

4 x CA: CALCIUM ION(Non-covalent)

CA.2: 3 residues within 4Å: Chain A: G.30, I.32, S.35 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:G.30, A:I.32, H2O.3, H2O.4, H2O.6 CA.3: 2 residues within 4Å: Chain A: D.53, E.91 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.53, A:D.53, A:E.91, A:E.91, H2O.6 CA.4: 4 residues within 4Å: Chain A: D.99, D.101 Ligands: APC.1, CA.5 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.99, A:D.101, H2O.3, H2O.7 CA.5: 4 residues within 4Å: Chain A: D.99, D.101 Ligands: APC.1, CA.4 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.99, A:D.101, H2O.5

3 x NA: SODIUM ION(Non-functional Binders)

NA.6: 1 residues within 4Å: Chain A: D.143 3 PLIP interactions: 3 interactions with chain A Water bridges: A:K.123, A:K.123, A:D.143 NA.7: 1 residues within 4Å: Chain A: M.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:M.4, A:M.4 NA.8: 2 residues within 4Å: Chain A: E.34, S.67 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.67

1 x 5RZ: 2-azanyl-8-[2-(4-bromophenyl)-2-oxidanylidene-ethyl]sulfanyl-1,9-dihydropurin-6-one(Non-covalent)

5RZ.9: 12 residues within 4Å: Chain A: T.46, P.47, P.48, L.49, G.50, Y.57, N.59, W.93, D.121, R.125, F.127 Ligands: APC.1 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:L.49, A:W.93, A:W.93 Hydrogen bonds: A:T.46, A:P.47, A:L.49, A:L.49, A:N.59, A:N.59 Water bridges: A:R.96 pi-Stacking: A:Y.57, A:Y.57, A:F.127 pi-Cation interactions: A:F.127

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.10: 4 residues within 4Å: Chain A: R.86, V.87, R.96, T.97 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dennis, M.L. et al., Structural Basis for the Selective Binding of Inhibitors to 6-Hydroxymethyl-7,8-dihydropterin Pyrophosphokinase from Staphylococcus aureus and Escherichia coli. J.Med.Chem. (2016)

Release Date

2016-05-04

Peptides

2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase

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