SMTL ID : 4dlk.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.02 Å

Oligo State

homo-dimer

Ligands

5 x CA: CALCIUM ION(Non-covalent)

CA.1: 3 residues within 4Å: Chain A: E.268 Ligands: CA.2, ATP.4 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.268, A:E.268, H2O.1, H2O.2, H2O.2 CA.2: 5 residues within 4Å: Chain A: E.255, E.268 Ligands: CA.1, ATP.4, ATP.5 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.255, A:E.255, A:E.268, H2O.2, H2O.3 CA.3: 3 residues within 4Å: Chain A: D.154 Ligands: ATP.4, ATP.5 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.154, H2O.2, H2O.2, H2O.2 CA.8: 3 residues within 4Å: Chain B: E.255, E.268 Ligands: ATP.10 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.255, B:E.255, B:E.268, H2O.9 CA.9: 3 residues within 4Å: Chain B: G.152, E.268 Ligands: ATP.10 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:G.152, B:E.268

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

ATP.4: 21 residues within 4Å: Chain A: R.107, V.145, K.147, G.152, Y.153, D.154, G.155, Q.158, E.182, K.183, W.184, V.185, F.187, E.190, F.257, N.267, E.268 Ligands: CA.1, CA.2, CA.3, ATP.5 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:K.147, A:D.154, A:D.154, A:G.155, A:Q.158, A:E.182, A:V.185, A:E.190, A:N.267, A:E.268 Water bridges: A:R.107, A:R.107, A:R.107, A:E.268, A:E.268 Salt bridges: A:R.107, A:R.107, A:K.147 pi-Stacking: A:W.184 ATP.5: 16 residues within 4Å: Chain A: Q.18, L.19, E.76, F.77, Y.153, H.213, L.218, E.255, R.272, H.274, N.275, K.348 Ligands: CA.2, CA.3, ATP.4, ATP.6 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:Q.18, A:Y.153, A:H.213, A:R.272, A:N.275 Water bridges: A:E.78, A:E.78, A:D.154, A:E.255, A:R.272, A:R.272, A:H.274, A:K.348, A:K.348 Salt bridges: A:R.272, A:R.272, A:H.274, A:H.274, A:K.348, A:K.348, A:K.348 ATP.6: 5 residues within 4Å: Chain A: F.77, N.79, K.340, R.347 Ligands: ATP.5 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:E.78, A:N.79, A:N.79 Water bridges: A:K.340, A:K.340, A:K.340 Salt bridges: A:K.340, A:R.347, A:R.347 ATP.10: 22 residues within 4Å: Chain B: R.107, V.145, K.147, G.152, Y.153, D.154, G.155, Q.158, E.182, K.183, W.184, V.185, F.187, E.190, H.213, N.216, E.255, F.257, N.267, E.268 Ligands: CA.8, CA.9 20 PLIP interactions: 20 interactions with chain B Hydrogen bonds: B:K.147, B:D.154, B:D.154, B:G.155, B:Q.158, B:E.182, B:E.182, B:V.185, B:E.190, B:H.213, B:N.267 Water bridges: B:R.107, B:R.107, B:N.216, B:E.255, B:H.274 Salt bridges: B:R.107, B:R.107, B:K.147 pi-Stacking: B:W.184

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.7: 8 residues within 4Å: Chain A: A.46, Q.47, V.48, A.49, D.50 Chain B: Q.47, V.48, A.49 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.47, A:A.49, B:A.49

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

2013-02-06

Peptides

Phosphoribosylaminoimidazole carboxylase, ATPase subunit: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Phosphoribosylaminoimidazole carboxylase, ATPase subunit