SMTL ID : 1tmm.1 (1 other biounit)

Crystal structure of ternary complex of E.coli HPPK(W89A) with MGAMPCPP and 6-Hydroxymethylpterin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.25 Å

Oligo State

monomer

Ligands

3 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.95, D.97 Ligands: MG.2, APC.9 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.95, A:D.97, H2O.1, H2O.1 MG.2: 5 residues within 4Å: Chain A: D.95, D.97 Ligands: MG.1, APC.9, HHR.10 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.95, A:D.97, H2O.3 MG.3: 3 residues within 4Å: Chain A: G.26, I.28, S.31 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:G.26, H2O.4, H2O.6, H2O.6, H2O.6

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

CL.4: 5 residues within 4Å: Chain A: P.114, K.119, F.137, P.138, D.139 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain A: R.82, V.83, R.84 Ligand excluded by PLIP

3 x ACT: ACETATE ION(Non-functional Binders)

ACT.5: 2 residues within 4Å: Chain A: H.148, T.149 No protein-ligand interaction detected (PLIP) ACT.6: 4 residues within 4Å: Chain A: E.30, S.31, H.32, E.61 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.32 Water bridges: A:E.30, A:E.30 Salt bridges: A:H.32 ACT.7: 2 residues within 4Å: Chain A: K.119 Ligands: GOL.11 3 PLIP interactions: 3 interactions with chain A Water bridges: A:K.119, A:D.139 Salt bridges: A:K.119

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

APC.9: 20 residues within 4Å: Chain A: L.70, Q.74, R.82, K.85, A.86, R.92, D.95, L.96, D.97, I.98, R.110, L.111, T.112, V.113, H.115, Y.116, R.121 Ligands: MG.1, MG.2, HHR.10 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:Q.74, A:R.82, A:R.82, A:A.86, A:R.92, A:I.98, A:T.112, A:T.112 Water bridges: A:Q.74, A:K.85, A:E.87, A:R.92, A:R.121 Salt bridges: A:H.115, A:R.121

1 x HHR: 6-HYDROXYMETHYLPTERIN(Non-covalent)

HHR.10: 11 residues within 4Å: Chain A: T.42, P.43, P.44, L.45, Y.53, N.55, R.92, D.95, F.123 Ligands: MG.2, APC.9 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:T.42, A:P.43, A:L.45, A:N.55, A:N.55, A:R.92 Water bridges: A:R.121, A:R.121 pi-Stacking: A:Y.53, A:F.123 pi-Cation interactions: A:F.123

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.11: 3 residues within 4Å: Chain A: T.112, Y.116 Ligands: ACT.7 1 PLIP interactions: 1 interactions with chain A Water bridges: A:P.114

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, Y. et al., Is the Critical Role of Loop 3 of Escherichia coli 6-Hydroxymethyl-7,8-dihydropterin Pyrophosphokinase in Catalysis Due to Loop-3 Residues Arginine-84 and Tryptophan-89? Site-Directed Mutagenesis, Biochemical, and Crystallographic Studies. Biochemistry (2005)

Release Date

2005-06-21

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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