SMTL ID : 3v4s.1

Crystal Structure of ADP-ATP complex of purK: N5-carboxyaminoimidazole ribonucleotide synthetase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.02 Å

Oligo State

homo-dimer

Ligands

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

ADP.1: 18 residues within 4Å: Chain A: R.113, V.151, K.153, Y.159, D.160, G.161, Q.164, E.188, K.189, W.190, V.191, F.193, E.196, N.222, F.263, N.273, E.274 Ligands: MG.2 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:K.153, A:G.158, A:G.161, A:Q.164, A:E.188, A:V.191, A:E.196, A:N.222, A:N.222, A:N.273 Water bridges: A:R.113, A:E.188, A:E.196 Salt bridges: A:R.113, A:R.113, A:K.153 pi-Stacking: A:W.190

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: E.261, E.274 Ligands: ADP.1 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.274, H2O.9, H2O.9 MG.5: 4 residues within 4Å: Chain B: E.261, N.273, E.274 Ligands: ATP.4 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.261, B:E.261, B:E.274, H2O.15 MG.6: 3 residues within 4Å: Chain B: T.110, E.116, L.275 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:T.110, B:E.116, B:L.275, H2O.14, H2O.15

2 x CO3: CARBONATE ION(Non-functional Binders)

CO3.3: 4 residues within 4Å: Chain A: R.278, H.280, N.281, K.354 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.278, A:R.278 Water bridges: A:D.160, A:K.354 CO3.7: 4 residues within 4Å: Chain B: R.278, H.280, N.281, K.354 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.278, B:R.278 Water bridges: B:D.160, B:K.354, B:K.354

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

ATP.4: 20 residues within 4Å: Chain B: R.113, K.153, G.158, Y.159, D.160, G.161, Q.164, E.188, K.189, W.190, V.191, F.193, E.196, H.219, N.222, E.261, F.263, N.273, E.274 Ligands: MG.5 22 PLIP interactions: 22 interactions with chain B Hydrogen bonds: B:K.153, B:D.160, B:G.161, B:Q.164, B:E.188, B:E.188, B:V.191, B:E.196, B:H.219, B:N.273 Water bridges: B:R.113, B:R.113, B:R.113, B:G.158, B:D.160, B:N.222, B:N.222, B:E.274 Salt bridges: B:R.113, B:R.113, B:K.153 pi-Stacking: B:W.190

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tuntland, M.L. et al., Elucidation of the bicarbonate binding site and insights into the carboxylation mechanism of (N(5))-carboxyaminoimidazole ribonucleotide synthase (PurK) from Bacillus anthracis. Acta Crystallogr.,Sect.D (2014)

Release Date

2013-02-13

Peptides

Phosphoribosylaminoimidazole carboxylase, ATPase subunit: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Phosphoribosylaminoimidazole carboxylase, ATPase subunit