SMTL ID : 2nsy.1

CRYSTAL STRUCTURE OF NH3-DEPENDENT NAD+ SYNTHETASE FROM BACILLUS SUBTILIS IN COMPLEX WITH NAD-ADENYLATE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.50, E.162 Ligands: AMP.3, POP.5 4 PLIP interactions: 2 interactions with chain A, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: A:D.50, A:E.162, AMP.3, H2O.7 MG.2: 3 residues within 4Å: Chain A: T.208 Ligands: AMP.3, POP.5 4 PLIP interactions: 1 interactions with chain A, 1 Ligand-Ligand interactions, 2 Ligand-Water interactions Metal complexes: A:T.208, AMP.3, H2O.7, H2O.7 MG.7: 3 residues within 4Å: Chain B: T.208 Ligands: AMP.9, POP.11 4 PLIP interactions: 1 interactions with chain B, 1 Ligand-Ligand interactions, 2 Ligand-Water interactions Metal complexes: B:T.208, AMP.9, H2O.16, H2O.17 MG.8: 4 residues within 4Å: Chain B: D.50, E.162 Ligands: AMP.9, POP.11 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.9, H2O.16

2 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.3: 19 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, MG.2, NAD.4, POP.5 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:S.51, A:R.78, A:L.79, A:Q.84 Water bridges: A:S.46, A:S.46, A:S.46, A:R.139, A:Q.143, A:T.157, A:T.157, A:E.162, A:E.162 AMP.9: 19 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.7, MG.8, NAD.10, POP.11 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:R.78, B:L.79, B:Q.84, B:R.139, B:T.157 Water bridges: B:S.46, B:S.46, B:D.50, B:D.50, B:R.139, B:Q.143

2 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.4: 20 residues within 4Å: Chain A: F.129, N.133, R.137, F.167, F.168, T.169, K.170, D.173, A.209, L.211, D.220, E.223, H.257, K.258 Chain B: Y.32, T.36, Y.144, L.153, D.177 Ligands: AMP.3 18 PLIP interactions: 16 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:A.209, A:L.211 Hydrogen bonds: A:N.133, A:K.170, A:K.170, B:Y.32, B:L.152 Water bridges: A:R.137, A:R.137, A:Q.218, A:E.223, A:E.223, A:H.257 Salt bridges: A:R.137, A:K.258, A:K.258 pi-Stacking: A:H.257, A:H.257 NAD.10: 19 residues within 4Å: Chain A: Y.32, T.36, Y.144, L.153, D.177 Chain B: N.133, R.137, F.167, F.168, T.169, K.170, D.173, A.209, L.211, D.220, E.223, H.257, K.258 Ligands: AMP.9 15 PLIP interactions: 13 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:A.209, B:L.211 Hydrogen bonds: B:N.133, B:K.170, B:K.170, B:E.223, A:Y.32, A:L.152 Water bridges: B:R.137, B:R.137 Salt bridges: B:R.137, B:K.258, B:K.258 pi-Stacking: B:H.257, B:H.257

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

POP.5: 12 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, MG.2, AMP.3 12 PLIP interactions: 12 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.157, A:E.162, A:T.208 Water bridges: A:T.157, A:K.186 Salt bridges: A:K.186 POP.11: 12 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.7, MG.8, AMP.9 14 PLIP interactions: 14 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:D.50, B:S.51, B:T.157, B:T.208 Water bridges: B:K.186, B:A.209, B:D.220 Salt bridges: B:K.186

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 7 residues within 4Å: Chain A: D.158, A.163, F.168, L.179, K.258, R.259 Chain B: P.262 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.258 Water bridges: A:G.174 GOL.12: 6 residues within 4Å: Chain A: P.262 Chain B: D.158, F.168, G.174, L.179, K.258 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.258 Water bridges: B:D.173, B:G.174, B:K.258, B:Q.260

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rizzi, M. et al., A novel deamido-NAD+-binding site revealed by the trapped NAD-adenylate intermediate in the NAD+ synthetase structure. Structure (1998)

Release Date

1999-01-13

Peptides

PROTEIN (NAD SYNTHETASE): AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

PROTEIN (NAD SYNTHETASE)

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