SMTL ID : 1xng.1

Crystal Structure of NH3-dependent NAD+ synthetase from Helicobacter pylori

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: S.183 Ligands: ATP.3 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.183, H2O.1, H2O.3 MG.4: 3 residues within 4Å: Chain B: S.33, S.183 Ligands: ATP.6 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:S.183

2 x DND: NICOTINIC ACID ADENINE DINUCLEOTIDE(Non-covalent)

DND.2: 24 residues within 4Å: Chain A: T.104, N.108, R.112, E.137, Y.142, G.143, T.144, L.145, D.148, A.184, L.186, Q.190, N.244, F.246, K.247 Chain B: R.23, F.25, Y.119, S.122, L.123, S.127, L.128, A.152 Ligands: ATP.3 25 PLIP interactions: 6 interactions with chain B, 19 interactions with chain A Hydrogen bonds: B:S.122, B:S.122, A:N.108, A:G.143, A:L.145, A:D.148, A:N.244 Water bridges: B:R.23, B:Y.119, B:Y.119, B:V.129, A:T.104, A:R.112, A:Q.190, A:Q.190, A:K.243, A:K.243 Hydrophobic interactions: A:A.184, A:L.186 Salt bridges: A:R.112, A:K.247, A:K.247 pi-Stacking: A:Y.142, A:F.246, A:F.246 DND.5: 24 residues within 4Å: Chain A: R.23, F.25, Y.119, S.122, L.123, S.127, L.128, A.152 Chain B: T.104, N.108, R.112, G.141, Y.142, G.143, T.144, L.145, D.148, A.184, L.186, Q.190, D.195, F.246, K.247 Ligands: ATP.6 24 PLIP interactions: 18 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:A.184, B:L.186 Hydrogen bonds: B:N.108, B:G.143, B:L.145, B:D.148, A:S.122, A:S.122 Water bridges: B:E.137, B:E.137, B:Q.190, B:D.195, B:D.195, B:K.247, A:R.23, A:R.23, A:R.23, A:V.129 Salt bridges: B:R.112, B:K.247, B:K.247 pi-Stacking: B:Y.142, B:F.246, B:F.246

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

ATP.3: 21 residues within 4Å: Chain A: G.31, L.32, S.33, G.35, L.36, D.37, S.38, L.56, L.57, M.58, P.59, R.114, T.132, E.137, D.148, K.161, P.182, S.183, A.184 Ligands: MG.1, DND.2 24 PLIP interactions: 24 interactions with chain A Hydrogen bonds: A:G.31, A:S.33, A:G.35, A:L.36, A:D.37, A:S.38, A:M.58, A:S.63, A:S.63, A:R.114, A:T.132, A:S.183 Water bridges: A:D.37, A:D.37, A:R.114, A:T.132, A:T.132, A:N.134, A:E.137, A:K.161, A:K.161, A:D.192 Salt bridges: A:K.161, A:K.161 ATP.6: 21 residues within 4Å: Chain B: G.31, L.32, S.33, G.35, L.36, D.37, S.38, L.56, L.57, M.58, P.59, R.114, T.132, E.137, D.148, K.161, P.182, S.183, A.184 Ligands: MG.4, DND.5 20 PLIP interactions: 20 interactions with chain B Hydrogen bonds: B:G.31, B:S.33, B:G.35, B:L.36, B:D.37, B:D.37, B:S.38, B:M.58, B:S.63, B:S.63, B:R.114, B:T.132, B:S.183, B:S.183 Water bridges: B:D.37, B:R.114, B:E.137, B:E.137, B:Y.200 Salt bridges: B:K.161

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kang, G.B. et al., Crystal structure of NH3-dependent NAD+ synthetase from Helicobacter pylori. Proteins (2005)

Release Date

2005-04-05

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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