SMTL ID : 1ytk.1

Crystal structure of a nicotinate phosphoribosyltransferase from Thermoplasma acidophilum with nicotinate mononucleotide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

homo-hexamer

Ligands

6 x NCN: NICOTINATE MONONUCLEOTIDE(Non-covalent)

NCN.1: 15 residues within 4Å: Chain A: F.144, R.147, R.148, S.170, V.183, G.184, T.185, R.241, D.243, G.277, G.278, G.298, T.299 Chain F: D.25, Y.27 14 PLIP interactions: 13 interactions with chain A, 1 interactions with chain F Hydrophobic interactions: A:F.144, F:Y.27 Hydrogen bonds: A:T.185, A:D.243, A:G.278, A:G.298, A:T.299, A:T.299, A:T.299 Water bridges: A:R.241, A:S.300 Salt bridges: A:R.148, A:R.241 pi-Stacking: A:F.144 NCN.3: 15 residues within 4Å: Chain B: F.144, R.147, R.148, S.170, V.183, G.184, T.185, R.241, D.243, G.277, G.278, G.298, T.299 Chain E: D.25, Y.27 14 PLIP interactions: 13 interactions with chain B, 1 interactions with chain E Hydrophobic interactions: B:F.144, E:Y.27 Hydrogen bonds: B:T.185, B:D.243, B:G.278, B:G.298, B:T.299, B:T.299, B:T.299 Water bridges: B:R.241, B:S.300 Salt bridges: B:R.148, B:R.241 pi-Stacking: B:F.144 NCN.5: 15 residues within 4Å: Chain C: F.144, R.147, R.148, S.170, V.183, G.184, T.185, R.241, D.243, G.277, G.278, G.298, T.299 Chain D: D.25, Y.27 14 PLIP interactions: 13 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:F.144, D:Y.27 Hydrogen bonds: C:T.185, C:D.243, C:G.278, C:G.298, C:T.299, C:T.299, C:T.299 Water bridges: C:R.241, C:S.300 Salt bridges: C:R.148, C:R.241 pi-Stacking: C:F.144 NCN.7: 15 residues within 4Å: Chain C: D.25, Y.27 Chain D: F.144, R.147, R.148, S.170, V.183, G.184, T.185, R.241, D.243, G.277, G.278, G.298, T.299 13 PLIP interactions: 12 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:F.144, C:Y.27 Hydrogen bonds: D:T.185, D:D.243, D:G.278, D:G.298, D:T.299, D:T.299 Water bridges: D:R.241, D:S.300 Salt bridges: D:R.148, D:R.241 pi-Stacking: D:F.144 NCN.9: 15 residues within 4Å: Chain B: D.25, Y.27 Chain E: F.144, R.147, R.148, S.170, V.183, G.184, T.185, R.241, D.243, G.277, G.278, G.298, T.299 13 PLIP interactions: 12 interactions with chain E, 1 interactions with chain B Hydrophobic interactions: E:F.144, B:Y.27 Hydrogen bonds: E:T.185, E:D.243, E:G.278, E:G.298, E:T.299, E:T.299 Water bridges: E:R.241, E:S.300 Salt bridges: E:R.148, E:R.241 pi-Stacking: E:F.144 NCN.11: 15 residues within 4Å: Chain A: D.25, Y.27 Chain F: F.144, R.147, R.148, S.170, V.183, G.184, T.185, R.241, D.243, G.277, G.278, G.298, T.299 13 PLIP interactions: 12 interactions with chain F, 1 interactions with chain A Hydrophobic interactions: F:F.144, A:Y.27 Hydrogen bonds: F:T.185, F:D.243, F:G.278, F:G.298, F:T.299, F:T.299 Water bridges: F:R.241, F:S.300 Salt bridges: F:R.148, F:R.241 pi-Stacking: F:F.144

6 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.2: 7 residues within 4Å: Chain A: T.56, G.124, T.127, K.128, K.131, K.305, F.307 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.305 Water bridges: A:D.55 TRS.4: 7 residues within 4Å: Chain B: T.56, G.124, T.127, K.128, K.131, K.305, F.307 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.305 Water bridges: B:D.55 TRS.6: 7 residues within 4Å: Chain C: T.56, G.124, T.127, K.128, K.131, K.305, F.307 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.305 Water bridges: C:D.55 TRS.8: 7 residues within 4Å: Chain D: T.56, G.124, T.127, K.128, K.131, K.305, F.307 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:K.305 Water bridges: D:D.55 TRS.10: 7 residues within 4Å: Chain E: T.56, G.124, T.127, K.128, K.131, K.305, F.307 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:K.305 Water bridges: E:D.55 TRS.12: 7 residues within 4Å: Chain F: T.56, G.124, T.127, K.128, K.131, K.305, F.307 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:K.305 Water bridges: F:D.55

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shin, D.H. et al., Crystal structure of a nicotinate phosphoribosyltransferase from Thermoplasma acidophilum. J.Biol.Chem. (2005)

Release Date

2005-03-08

Peptides

nicotinate phosphoribosyltransferase from Thermoplasma acidophilum: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

nicotinate phosphoribosyltransferase from Thermoplasma acidophilum

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