SMTL ID : 9iw1.1

wild type NMN/NaMN adenylyltransferase from Chaetomium thermophilum

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.11 Å

Oligo State

homo-dimer

Ligands

2 x NMN: BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE(Non-covalent)

NMN.1: 12 residues within 4Å: Chain A: C.71, G.72, S.73, V.108, Y.112, K.114, Y.155, P.157, T.158, L.196, L.205, W.206 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:C.71, A:S.73, A:Y.155, A:T.158, A:T.158, A:L.205 Water bridges: A:F.74, A:S.207, A:S.207, A:D.210, A:D.210, A:D.210 Salt bridges: A:K.114 pi-Stacking: A:W.206 NMN.7: 11 residues within 4Å: Chain B: C.71, G.72, S.73, V.108, Y.112, Y.155, P.157, T.158, L.196, L.205, W.206 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:L.205 Hydrogen bonds: B:C.71, B:S.73, B:Y.155, B:T.158, B:T.158, B:L.205 Water bridges: B:G.72, B:S.73, B:S.73, B:F.74, B:Y.112, B:S.199, B:S.207 pi-Stacking: B:W.206, B:W.206

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 9 residues within 4Å: Chain A: Q.58, Q.60, P.61, G.62, K.63, G.178, T.179, D.180, R.184 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.58, A:G.62, A:T.179, A:D.180 Water bridges: A:D.180 GOL.6: 7 residues within 4Å: Chain A: F.79, P.275, D.276, P.277 Chain B: F.79, P.275, D.276 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:D.276, A:D.276 Water bridges: B:D.276, B:D.276, A:I.274, A:D.276 GOL.8: 9 residues within 4Å: Chain B: Q.58, Q.60, P.61, G.62, K.63, G.178, T.179, D.180, R.184 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.58, B:G.62, B:T.179, B:T.179, B:D.180

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 6 residues within 4Å: Chain A: K.53, K.55, S.89, V.100, C.101, W.136 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.53, A:S.89, A:S.89 PEG.9: 6 residues within 4Å: Chain B: K.53, K.55, S.89, V.100, C.101, W.136 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.53, B:K.55, B:S.89 Water bridges: B:K.55, B:W.136

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

EDO.4: 3 residues within 4Å: Chain A: A.118, L.287, Y.288 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.288 EDO.5: 7 residues within 4Å: Chain A: D.166, N.170, A.186, R.187, I.188, Q.217, Y.218 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.188, A:I.188 EDO.10: 4 residues within 4Å: Chain B: R.238, I.244, W.245, V.246 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.238, B:R.238, B:V.246

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Qian, X.L. et al., Biochemical and structural characterization of a novel nicotinamide mononucleotide adenylyltransferase from thermophilic fungi Chaetomium thermophilum. Biochem.Biophys.Res.Commun. (2025)

Release Date

2025-06-25

Peptides

Nicotinamide-nucleotide adenylyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Nicotinamide-nucleotide adenylyltransferase