SMTL ID : 3etj.1

Crystal structure E. coli Purk in complex with Mg, ADP, and Pi

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 24 residues within 4Å: Chain A: R.80, I.118, K.120, G.125, Y.126, D.127, G.128, Q.131, R.133, E.153, Q.154, G.155, I.156, F.158, E.161, H.184, G.187, E.226, F.228, N.237, E.238 Ligands: MG.2, MG.3, PI.4 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:K.120, A:Y.126, A:D.127, A:G.128, A:Q.131, A:R.133, A:E.153, A:E.153, A:I.156, A:E.161, A:N.237, A:E.238 Water bridges: A:R.80, A:R.80, A:H.184, A:E.226 Salt bridges: A:R.80, A:R.80, A:K.120 ADP.6: 19 residues within 4Å: Chain B: R.80, I.118, K.120, Q.131, E.153, Q.154, G.155, I.156, F.158, E.161, H.184, G.187, E.226, F.228, N.237, E.238 Ligands: MG.7, MG.8, PI.9 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:K.120, B:Q.131, B:E.153, B:I.156, B:E.161, B:N.237, B:E.238 Water bridges: B:R.133, B:H.184, B:E.226 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, E.238 Ligands: ADP.1, MG.3, PI.4 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.226, A:E.238, H2O.12 MG.3: 4 residues within 4Å: Chain A: E.238 Ligands: ADP.1, MG.2, PI.4 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.238, A:E.238, H2O.9, H2O.12 MG.7: 5 residues within 4Å: Chain B: E.226, E.238 Ligands: ADP.6, MG.8, PI.9 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.226, B:E.238, H2O.25 MG.8: 4 residues within 4Å: Chain B: E.238 Ligands: ADP.6, MG.7, PI.9 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.238, B:E.238, H2O.25, H2O.25

2 x PI: HYDROGENPHOSPHATE ION(Non-covalent)

PI.4: 9 residues within 4Å: Chain A: Y.126, D.127, E.226, E.238, R.242, H.244 Ligands: ADP.1, MG.2, MG.3 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:D.127, A:E.238 Water bridges: A:E.238, A:R.242, A:R.242, A:K.314, A:K.314, A:K.314 Salt bridges: A:R.242, A:H.244, A:K.314 PI.9: 7 residues within 4Å: Chain B: E.226, E.238, R.242, H.244 Ligands: ADP.6, MG.7, MG.8 6 PLIP interactions: 6 interactions with chain B Water bridges: B:E.238, B:R.242, B:R.242 Salt bridges: B:R.242, B:H.244, B:K.314

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

CL.5: 4 residues within 4Å: Chain A: A.48, R.242, V.243, H.262 Ligand excluded by PLIP

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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