SMTL ID : 3eth.1

Crystal structure of E. coli Purk in complex with MgATP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 21 residues within 4Å: Chain A: R.80, I.118, K.120, G.125, Y.126, D.127, G.128, Q.131, E.153, Q.154, G.155, I.156, F.158, E.161, H.184, E.226, F.228, N.237, E.238 Ligands: MG.2, MG.3 25 PLIP interactions: 25 interactions with chain A Hydrogen bonds: A:K.120, A:D.127, A:G.128, A:Q.131, A:E.153, A:Q.154, A:I.156, A:E.161, A:N.237 Water bridges: A:R.80, A:R.80, A:D.127, A:H.184, A:L.189, A:E.226, A:R.242, A:K.314, A:K.314, A:K.314, A:K.314 Salt bridges: A:R.80, A:R.80, A:K.120 pi-Stacking: A:F.228, A:F.228 ATP.4: 21 residues within 4Å: Chain B: R.80, I.118, K.120, G.125, Y.126, D.127, G.128, Q.131, E.153, Q.154, G.155, I.156, F.158, E.161, H.184, E.226, F.228, N.237, E.238 Ligands: MG.5, MG.6 27 PLIP interactions: 27 interactions with chain B Hydrogen bonds: B:K.120, B:D.127, B:D.127, B:G.128, B:Q.131, B:Q.154, B:I.156, B:E.161, B:H.184, B:N.237 Water bridges: B:R.80, B:R.80, B:R.80, B:D.127, B:R.133, B:H.184, B:L.189, B:E.226, B:E.238, B:R.242, B:K.314, B:K.314, B:K.314, B:K.314 Salt bridges: B:R.80, B:R.80, B:K.120

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: E.226, N.237, E.238 Ligands: ATP.1, MG.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.226, A:E.226, A:E.238, H2O.13 MG.3: 4 residues within 4Å: Chain A: R.80, E.238 Ligands: ATP.1, MG.2 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.238, A:E.238, H2O.13, H2O.13 MG.5: 5 residues within 4Å: Chain B: E.226, N.237, E.238 Ligands: ATP.4, MG.6 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.226, B:E.226, B:E.238, H2O.24 MG.6: 4 residues within 4Å: Chain B: R.80, E.238 Ligands: ATP.4, MG.5 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.238, B:E.238, H2O.25, H2O.25

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Thoden, J.B. et al., Structural analysis of the active site geometry of N(5)-Carboxyaminoimidazole ribonucleotide synthetase from Escherichia coli. Biochemistry (2008)

Release Date

2008-10-21

Peptides

Phosphoribosylaminoimidazole carboxylase ATPase subunit: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Phosphoribosylaminoimidazole carboxylase ATPase subunit

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