SMTL ID : 2pza.1

NAD+ Synthetase from Bacillus anthracis with AMP + PPi and Mg2+

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.51, E.163 Ligands: AMP.3, POP.4 4 PLIP interactions: 2 interactions with chain A, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: A:D.51, A:E.163, AMP.3, H2O.5 MG.2: 5 residues within 4Å: Chain A: S.47, T.209, A.210 Ligands: AMP.3, POP.4 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.209, H2O.5, H2O.5 MG.6: 5 residues within 4Å: Chain B: S.47, T.209, A.210 Ligands: AMP.8, POP.9 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:T.209, H2O.9, H2O.9 MG.7: 4 residues within 4Å: Chain B: D.51, E.163 Ligands: AMP.8, POP.9 4 PLIP interactions: 2 interactions with chain B, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: B:D.51, B:E.163, AMP.8, H2O.9

2 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.3: 18 residues within 4Å: Chain A: L.44, G.45, I.46, S.47, S.52, V.78, R.79, L.80, Q.85, R.140, T.158, E.163, D.174, T.209, A.210 Ligands: MG.1, MG.2, POP.4 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:G.45, A:S.52, A:R.79, A:L.80, A:Q.85, A:R.140, A:T.158 Water bridges: A:S.47, A:S.47, A:S.47, A:D.51, A:D.51, A:R.140, A:T.209 AMP.8: 18 residues within 4Å: Chain B: L.44, G.45, I.46, S.47, S.52, V.78, R.79, L.80, Q.85, R.140, T.158, E.163, D.174, T.209, A.210 Ligands: MG.6, MG.7, POP.9 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:S.52, B:R.79, B:L.80, B:Q.85, B:R.140, B:T.209 Water bridges: B:S.47, B:S.47, B:S.47, B:R.140, B:T.158, B:T.158, B:T.209

2 x POP: PYROPHOSPHATE 2-(Non-covalent)

POP.4: 12 residues within 4Å: Chain A: S.47, G.49, Q.50, D.51, S.52, E.163, K.187, P.208, T.209 Ligands: MG.1, MG.2, AMP.3 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:S.47, A:S.47, A:Q.50, A:D.51, A:D.51, A:S.52, A:T.158, A:E.163, A:T.209 Water bridges: A:K.187, A:D.221, A:D.221 Salt bridges: A:K.187 POP.9: 12 residues within 4Å: Chain B: S.47, G.49, Q.50, D.51, S.52, E.163, K.187, P.208, T.209 Ligands: MG.6, MG.7, AMP.8 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:S.47, B:S.47, B:Q.50, B:D.51, B:S.52, B:T.209 Water bridges: B:T.158, B:T.209, B:D.221, B:D.221 Salt bridges: B:K.187

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 5 residues within 4Å: Chain A: Y.82, V.84, Q.85, K.86, D.211 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.82, A:K.86, A:D.211 Water bridges: A:Y.82 GOL.10: 5 residues within 4Å: Chain B: Y.82, V.84, Q.85, K.86, D.211 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:K.86 Water bridges: B:Y.82, B:Y.82, B:K.136, B:D.211, B:D.214

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

McDonald, H.M. et al., Structural adaptation of an interacting non-native C-terminal helical extension revealed in the crystal structure of NAD(+) synthetase from Bacillus anthracis. Acta Crystallogr.,Sect.D (2007)

Release Date

2007-07-31

Peptides

NH(3)-dependent NAD(+) synthetase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

NH(3)-dependent NAD(+) synthetase

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