SMTL ID : 1kqp.1

NH3-DEPENDENT NAD+ SYNTHETASE FROM BACILLUS SUBTILIS AT 1 A RESOLUTION

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.03 Å

Oligo State

homo-dimer

Ligands

5 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.50, E.162 Ligands: ADJ.6, POP.7 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.1, ADJ.6 MG.2: 6 residues within 4Å: Chain A: S.46, G.48, T.208, A.209 Ligands: ADJ.6, POP.7 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.208, H2O.2, H2O.5 MG.8: 6 residues within 4Å: Chain B: S.46, G.48, T.208, A.209 Ligands: ADJ.18, POP.19 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:T.208, H2O.15, H2O.15 MG.9: 4 residues within 4Å: Chain B: D.50, E.162 Ligands: ADJ.18, POP.19 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.50, B:E.162, H2O.14 MG.10: 1 residues within 4Å: Chain B: D.124 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.124, H2O.15, H2O.15, H2O.16

10 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 7 residues within 4Å: Chain A: G.225, I.226, E.230, K.243, V.244, A.247 Ligands: EDO.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.230, A:K.243 EDO.4: 6 residues within 4Å: Chain A: E.221, G.225, I.226, S.227, E.230 Ligands: EDO.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.221, A:S.227, A:E.230 EDO.5: 7 residues within 4Å: Chain A: V.261, P.262 Chain B: D.158, F.168, G.174, L.179, K.258 1 PLIP interactions: 1 interactions with chain B Water bridges: B:D.173 EDO.11: 2 residues within 4Å: Chain B: K.194, E.195 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.195 EDO.12: 3 residues within 4Å: Chain B: R.56, F.96, K.98 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:F.96, B:K.98 EDO.13: 6 residues within 4Å: Chain B: E.23, V.26, N.27, K.30, S.64 Ligands: EDO.14 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.23, B:N.27, B:S.64 Water bridges: B:K.30 EDO.14: 5 residues within 4Å: Chain B: K.30, S.64, E.67, E.68 Ligands: EDO.13 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.30, B:S.64, B:E.67 Water bridges: B:N.27, B:E.68 EDO.15: 4 residues within 4Å: Chain A: E.121, T.122 Chain B: W.103, K.104 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.104, B:K.104 EDO.16: 8 residues within 4Å: Chain A: L.179, T.182 Chain B: V.261, P.262, A.263, S.264, F.266, D.267 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.264, B:S.264 EDO.17: 6 residues within 4Å: Chain B: R.56, Q.59, L.60, E.63, I.97, K.98 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.56, B:R.56, B:K.98 Water bridges: B:E.63, B:E.63

2 x ADJ: NICOTINAMIDE-ADENINE-DINUCLEOTIDE-ADENYLATE INTERMEDIATE(Non-covalent)

ADJ.6: 41 residues within 4Å: Chain A: L.43, G.44, I.45, S.46, D.50, S.51, V.77, R.78, L.79, P.80, Q.84, F.129, N.133, A.136, R.137, R.139, Q.143, T.157, E.162, F.167, F.168, T.169, K.170, D.173, T.208, A.209, L.211, E.223, H.257, K.258 Chain B: Y.32, T.36, Y.144, G.148, L.152, L.153, V.154, D.177 Ligands: MG.1, MG.2, POP.7 42 PLIP interactions: 37 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:A.209, A:L.211 Hydrogen bonds: A:S.51, A:R.78, A:L.79, A:Q.84, A:Q.84, A:N.133, A:R.139, A:R.139, A:T.157, A:T.157, A:K.170, A:K.170, A:E.223, A:E.223, B:Y.32, B:Y.32, B:L.152 Water bridges: A:S.46, A:S.46, A:S.46, A:R.137, A:R.137, A:R.139, A:Q.143, A:E.162, A:E.162, A:E.162, A:F.167, A:Q.218, A:E.223, A:H.257, A:K.258, A:K.258, A:K.258, B:G.147, B:L.152 Salt bridges: A:R.137, A:K.258, A:K.258 pi-Stacking: A:H.257 ADJ.18: 41 residues within 4Å: Chain A: Y.32, T.36, Y.144, G.148, L.152, L.153, V.154, D.177 Chain B: L.43, G.44, I.45, S.46, D.50, S.51, V.77, R.78, L.79, P.80, Q.84, N.133, A.136, R.137, R.139, Q.143, T.157, E.162, F.167, F.168, T.169, K.170, D.173, T.208, A.209, L.211, E.223, R.251, H.257, K.258 Ligands: MG.8, MG.9, POP.19 38 PLIP interactions: 33 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:A.209, B:L.211 Hydrogen bonds: B:G.44, B:S.51, B:R.78, B:L.79, B:Q.84, B:Q.84, B:N.133, B:R.139, B:R.139, B:T.157, B:F.167, B:K.170, B:K.170, B:T.208, B:E.223, B:E.223, A:Y.32, A:Y.32, A:D.177 Water bridges: B:S.46, B:S.46, B:S.46, B:D.50, B:D.50, B:R.137, B:R.139, B:Q.143, B:K.258, B:K.258, A:Y.144, A:G.147 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.7: 14 residues within 4Å: Chain A: S.46, G.48, Q.49, D.50, S.51, T.52, T.157, E.162, K.186, P.207, T.208 Ligands: MG.1, MG.2, ADJ.6 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:S.46, A:G.48, A:Q.49, A:D.50, A:S.51, A:S.51, A:T.208 Water bridges: A:E.162, A:E.162, A:E.162 Salt bridges: A:K.186 POP.19: 13 residues within 4Å: Chain B: S.46, G.48, Q.49, D.50, S.51, T.52, E.162, K.186, P.207, T.208 Ligands: MG.8, MG.9, ADJ.18 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:S.46, B:G.48, B:Q.49, B:D.50, B:D.50, B:D.50, B:S.51, B:S.51, B:T.157, B:T.208, B:T.208 Water bridges: B:T.157, B:K.186 Salt bridges: B:K.186

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Symersky, J. et al., NH3-dependent NAD+ synthetase from Bacillus subtilis at 1 A resolution. Acta Crystallogr.,Sect.D (2002)

Release Date

2002-06-28

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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