SMTL ID : 5huh.1

Crystal Structure of NadE from Streptococcus pyogenes

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

13 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 7 residues within 4Å: Chain A: S.81, G.83, Q.84, D.85, S.86 Ligands: SO4.6, MG.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.81, A:D.85, A:S.86 SO4.2: 3 residues within 4Å: Chain A: H.293 Chain B: Y.66, L.73 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Salt bridges: A:H.293 Hydrogen bonds: B:Y.66 SO4.3: 7 residues within 4Å: Chain A: D.194, N.199, F.204, G.210, L.215, K.294 Chain B: P.298 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Water bridges: B:P.298 Hydrogen bonds: A:N.199 SO4.4: 3 residues within 4Å: Chain A: Y.118, K.171, R.175 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.118 Salt bridges: A:K.171, A:R.175 SO4.5: 5 residues within 4Å: Chain A: R.223, K.226, Y.264, Q.265, D.268 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.268 Water bridges: A:Q.265 Salt bridges: A:R.223, A:K.226 SO4.6: 6 residues within 4Å: Chain A: G.83, Q.84, D.85, K.222 Ligands: SO4.1, MG.8 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.84, A:D.85 Water bridges: A:K.222, A:K.222 Salt bridges: A:K.222 SO4.7: 4 residues within 4Å: Chain A: S.49, I.50, Q.224, A.227 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.50, A:Q.224 SO4.9: 7 residues within 4Å: Chain A: P.298 Chain B: D.194, N.199, F.204, G.210, L.215, K.294 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.199, B:G.210 SO4.10: 7 residues within 4Å: Chain B: S.81, G.83, Q.84, D.85, S.86 Ligands: SO4.11, MG.15 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.81, B:S.81, B:G.83, B:D.85, B:D.85, B:S.86 SO4.11: 7 residues within 4Å: Chain B: G.83, Q.84, D.85, K.222, D.256 Ligands: SO4.10, MG.15 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.84 Salt bridges: B:K.222 SO4.12: 6 residues within 4Å: Chain B: K.222, R.223, K.226, Y.264, Q.265, D.268 4 PLIP interactions: 4 interactions with chain B Water bridges: B:R.223, B:R.223 Salt bridges: B:R.223, B:K.226 SO4.13: 2 residues within 4Å: Chain B: V.258, G.261 No protein-ligand interaction detected (PLIP) SO4.14: 3 residues within 4Å: Chain B: L.36, Q.281, E.285 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.281, B:E.285 Water bridges: B:L.36

2 x MG: MAGNESIUM ION(Non-covalent)

MG.8: 4 residues within 4Å: Chain A: D.85, E.198 Ligands: SO4.1, SO4.6 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.85, A:E.198, H2O.1, H2O.3, H2O.3 MG.15: 4 residues within 4Å: Chain B: D.85, E.198 Ligands: SO4.10, SO4.11 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.85, B:E.198, H2O.5, H2O.7, H2O.7

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Booth, W.T. et al., Streptococcus pyogenes quinolinate-salvage pathway-structural and functional studies of quinolinate phosphoribosyl transferase and NH3 -dependent NAD(+) synthetase. FEBS J. (2017)

Release Date

2017-01-25

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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