SMTL ID : 3r5h.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

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

ADP.1: 17 residues within 4Å: Chain A: R.113, V.151, K.153, 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.3 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:K.153, A:Q.164, A:E.188, A:V.191, A:E.196, A:N.222, A:N.273 Water bridges: A:E.196, A:H.219, A:H.219, A:N.222, A:N.222, A:N.222 Salt bridges: A:R.113, A:R.113, A:K.153 pi-Stacking: A:W.190 ADP.4: 16 residues within 4Å: Chain B: R.113, V.151, K.153, Q.164, E.188, K.189, W.190, V.191, F.193, E.196, H.219, N.222, F.263, N.273, E.274 Ligands: MG.6 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:K.153, B:Q.164, B:E.188, B:E.188, B:V.191, B:E.196, B:H.219, B:N.222, B:N.273 Water bridges: B:R.113, B:R.113, B:K.117, B:E.274 Salt bridges: B:R.113, B:R.113, B:K.153

2 x AIR: 5-AMINOIMIDAZOLE RIBONUCLEOTIDE(Non-covalent)

AIR.2: 9 residues within 4Å: Chain A: G.23, Q.24, L.25, E.82, E.84, Y.159, R.278, K.346, R.353 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:G.23, A:Q.24, A:Q.24, A:L.25, A:E.82, A:E.84 Water bridges: A:R.278, A:K.346, A:K.346, A:K.346, A:K.346 Salt bridges: A:K.346, A:R.353 AIR.5: 8 residues within 4Å: Chain B: G.23, Q.24, L.25, E.82, F.83, R.278, K.346, R.353 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:G.23, B:Q.24, B:L.25, B:E.82 Water bridges: B:R.278, B:R.278, B:K.346, B:K.346, B:K.346, B:R.353, B:K.354, B:K.354 Salt bridges: B:K.346, B:R.353

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: E.261, N.273, E.274 Ligands: ADP.1 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.274, H2O.1, H2O.8, H2O.11 MG.6: 3 residues within 4Å: Chain B: E.261, E.274 Ligands: ADP.4 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.261, B:E.274, H2O.19, H2O.20

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

2012-03-21

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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