SMTL ID : 1nsy.1

CRYSTAL STRUCTURE OF NH3-DEPENDENT NAD+ SYNTHETASE FROM BACILLUS SUBTILIS

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.50, E.162 Ligands: AMP.3, POP.4 4 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:D.50, A:E.162, H2O.2, AMP.3 MG.5: 4 residues within 4Å: Chain B: D.50, E.162 Ligands: AMP.7, POP.8 4 PLIP interactions: 2 interactions with chain B, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: B:D.50, B:E.162, AMP.7, H2O.9

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

ATP.2: 14 residues within 4Å: Chain A: F.129, N.133, R.137, F.168, T.169, K.170, H.257, K.258 Chain B: Y.32, T.36, Y.144, L.152, L.153, D.177 15 PLIP interactions: 3 interactions with chain B, 12 interactions with chain A Hydrogen bonds: B:Y.32, B:L.152, A:N.133, A:K.170, A:K.170 Water bridges: B:Y.144, A:R.137, A:R.251, A:H.257 Salt bridges: A:R.137, A:K.258, A:K.258, A:K.258 pi-Stacking: A:H.257, A:H.257 ATP.6: 14 residues within 4Å: Chain A: Y.32, T.36, Y.144, L.152, L.153, D.177 Chain B: F.129, N.133, R.137, F.168, T.169, K.170, H.257, K.258 13 PLIP interactions: 11 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:N.133, B:F.168, B:K.170, A:Y.32, A:L.152 Water bridges: B:K.170, B:H.257 Salt bridges: B:R.137, B:K.258, B:K.258, B:K.258 pi-Stacking: B:H.257, B:H.257

2 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.3: 17 residues within 4Å: Chain A: L.43, G.44, I.45, S.46, S.51, V.77, R.78, L.79, Q.84, R.139, T.157, E.162, D.173, T.208, A.209 Ligands: MG.1, POP.4 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:S.51, A:R.78, A:L.79, A:Q.84, A:T.208 Water bridges: A:R.139, A:R.139, A:T.157, A:T.157 AMP.7: 17 residues within 4Å: Chain B: L.43, G.44, I.45, S.46, S.51, V.77, R.78, L.79, Q.84, R.139, T.157, E.162, D.173, T.208, A.209 Ligands: MG.5, POP.8 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:S.51, B:R.78, B:R.78, B:L.79, B:Q.84, B:R.139, B:T.157, B:T.208 Water bridges: B:S.46, B:S.46, B:D.50, B:D.50, B:R.139

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

POP.4: 11 residues within 4Å: Chain A: S.46, G.48, Q.49, D.50, S.51, E.162, K.186, P.207, T.208 Ligands: MG.1, AMP.3 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:S.46, A:S.46, A:G.48, A:Q.49, A:D.50, A:S.51, A:T.208 Water bridges: A:T.157, A:E.162 Salt bridges: A:K.186 POP.8: 11 residues within 4Å: Chain B: S.46, G.48, Q.49, D.50, S.51, E.162, K.186, P.207, T.208 Ligands: MG.5, AMP.7 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:S.46, B:S.46, B:G.48, B:Q.49, B:D.50, B:D.50, B:S.51, B:T.208 Water bridges: B:K.186 Salt bridges: B:K.186

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rizzi, M. et al., Crystal structure of NH3-dependent NAD+ synthetase from Bacillus subtilis. EMBO J. (1996)

Release Date

1997-07-23

Peptides

NAD SYNTHETASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

NAD SYNTHETASE

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