SMTL ID : 3nm1.1

The Crystal Structure of Candida glabrata THI6, a Bifunctional Enzyme involved in Thiamin Biosyhthesis of Eukaryotes

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.21 Å

Oligo State

homo-hexamer

Ligands

6 x 3NM: 4-methyl-5-[2-(phosphonooxy)ethyl]-1,3-thiazole-2-carboxylic acid(Non-covalent)

3NM.1: 14 residues within 4Å: Chain A: R.45, G.138, T.139, T.143, T.145, K.146, K.151, I.179, G.180, G.181, V.209, S.210 Ligands: IFP.2, POP.3 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:T.145 Hydrogen bonds: A:T.143, A:T.145, A:T.145, A:G.181, A:V.209, A:S.210 Salt bridges: A:K.146, A:K.151 3NM.5: 12 residues within 4Å: Chain B: R.45, G.138, T.139, T.143, T.145, K.151, I.179, G.181, V.208, V.209, S.210 Ligands: IFP.6 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:T.145, B:V.209 Hydrogen bonds: B:T.143, B:T.145, B:G.181, B:V.209, B:S.210 Salt bridges: B:K.151 3NM.9: 13 residues within 4Å: Chain C: R.45, G.138, T.139, T.143, T.145, K.151, I.179, G.180, G.181, V.209, S.210 Ligands: IFP.10, POP.11 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:T.145 Hydrogen bonds: C:T.145, C:T.145, C:G.181, C:V.209, C:S.210 Salt bridges: C:K.146, C:K.151 3NM.13: 14 residues within 4Å: Chain D: R.45, G.138, T.139, T.143, T.145, K.146, K.151, I.179, G.180, G.181, V.209, S.210 Ligands: IFP.14, POP.15 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:T.145 Hydrogen bonds: D:T.145, D:G.181, D:V.209, D:S.210 Salt bridges: D:K.146, D:K.151 3NM.17: 13 residues within 4Å: Chain E: R.45, G.138, T.139, T.143, T.145, K.151, I.179, G.181, V.208, V.209, S.210 Ligands: IFP.18, POP.19 8 PLIP interactions: 8 interactions with chain E Hydrophobic interactions: E:T.145 Hydrogen bonds: E:T.145, E:T.145, E:G.181, E:V.209, E:S.210 Salt bridges: E:K.146, E:K.151 3NM.21: 14 residues within 4Å: Chain F: R.45, G.138, T.139, T.143, T.145, K.146, K.151, I.179, G.180, G.181, V.209, S.210 Ligands: IFP.22, POP.23 8 PLIP interactions: 8 interactions with chain F Hydrophobic interactions: F:T.145 Hydrogen bonds: F:G.180, F:G.181, F:V.209, F:S.210, F:S.210 Salt bridges: F:K.146, F:K.151

6 x IFP: 2-TRIFLUOROMETHYL-5-METHYLENE-5H-PYRIMIDIN-4-YLIDENEAMINE(Non-covalent)

IFP.2: 13 residues within 4Å: Chain A: Y.13, Q.43, N.75, H.90, S.114, Y.134, G.136, K.146, V.177, I.179, C.207 Ligands: 3NM.1, POP.3 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.179 Hydrogen bonds: A:Q.43 pi-Stacking: A:H.90 Halogen bonds: A:Q.43, A:C.207 IFP.6: 14 residues within 4Å: Chain B: Y.13, V.15, Q.43, R.45, N.75, H.90, S.114, Y.134, G.136, V.177, I.179, C.207 Ligands: 3NM.5, POP.7 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:I.179 Hydrogen bonds: B:Q.43, B:Q.43, B:N.75 pi-Cation interactions: B:H.90 Halogen bonds: B:Y.134, B:C.207 IFP.10: 13 residues within 4Å: Chain C: Y.13, V.15, Q.43, N.75, H.90, S.114, Y.134, G.136, V.177, I.179, C.207 Ligands: 3NM.9, POP.11 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:I.179 Hydrogen bonds: C:Q.43, C:Q.43 pi-Cation interactions: C:H.90 Halogen bonds: C:Y.134 IFP.14: 12 residues within 4Å: Chain D: Y.13, V.15, Q.43, H.90, S.114, Y.134, G.136, V.177, I.179, C.207 Ligands: 3NM.13, POP.15 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:I.179 Hydrogen bonds: D:Q.43, D:Q.43 pi-Cation interactions: D:H.90 Halogen bonds: D:Y.134 IFP.18: 13 residues within 4Å: Chain E: Y.13, V.15, Q.43, N.75, H.90, S.114, Y.134, G.136, V.177, I.179, C.207 Ligands: 3NM.17, POP.19 5 PLIP interactions: 5 interactions with chain E Hydrophobic interactions: E:I.179 Hydrogen bonds: E:Q.43, E:Q.43 pi-Stacking: E:H.90 Halogen bonds: E:Y.134 IFP.22: 12 residues within 4Å: Chain F: Y.13, Q.43, N.75, H.90, S.114, Y.134, G.136, V.177, I.179, C.207 Ligands: 3NM.21, POP.23 5 PLIP interactions: 5 interactions with chain F Hydrophobic interactions: F:I.179 Hydrogen bonds: F:Q.43, F:Q.43 pi-Stacking: F:H.90 Halogen bonds: F:C.207

6 x POP: PYROPHOSPHATE 2-(Non-covalent)

POP.3: 12 residues within 4Å: Chain A: R.45, K.47, N.75, D.76, V.91, G.92, D.95, S.114, K.146 Ligands: 3NM.1, IFP.2, MG.4 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:N.75, A:N.75, A:D.76, A:S.114 Salt bridges: A:R.45, A:K.47, A:K.47, A:K.146, A:K.146 POP.7: 9 residues within 4Å: Chain B: R.45, K.47, N.75, G.92, D.95, S.114, K.146 Ligands: IFP.6, MG.8 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:N.75, B:N.75, B:S.114, B:S.114 Salt bridges: B:R.45, B:K.47, B:K.47, B:K.146, B:K.146 POP.11: 11 residues within 4Å: Chain C: R.45, K.47, N.75, D.76, G.92, D.95, S.114, K.146 Ligands: 3NM.9, IFP.10, MG.12 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:N.75, C:N.75, C:S.114 Salt bridges: C:R.45, C:K.47, C:K.146, C:K.146 POP.15: 11 residues within 4Å: Chain D: R.45, K.47, N.75, D.76, G.92, D.95, S.114, K.146 Ligands: 3NM.13, IFP.14, MG.16 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:N.75, D:N.75, D:N.75, D:D.95, D:S.114 Salt bridges: D:R.45, D:K.47, D:K.146, D:K.146 POP.19: 11 residues within 4Å: Chain E: R.45, K.47, N.75, D.76, G.92, D.95, S.114, K.146 Ligands: 3NM.17, IFP.18, MG.20 9 PLIP interactions: 9 interactions with chain E Hydrogen bonds: E:N.75, E:N.75, E:N.75, E:G.92, E:S.114 Salt bridges: E:R.45, E:K.47, E:K.146, E:K.146 POP.23: 11 residues within 4Å: Chain F: R.45, K.47, N.75, D.76, G.92, D.95, S.114, K.146 Ligands: 3NM.21, IFP.22, MG.24 9 PLIP interactions: 9 interactions with chain F Hydrogen bonds: F:N.75, F:N.75, F:N.75, F:S.114, F:S.114 Salt bridges: F:R.45, F:K.47, F:K.146, F:K.146

6 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 5 residues within 4Å: Chain A: K.47, N.75, D.76, D.95 Ligands: POP.3 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.76, A:D.95 MG.8: 5 residues within 4Å: Chain B: K.47, N.75, D.76, D.95 Ligands: POP.7 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.95, B:D.95 MG.12: 4 residues within 4Å: Chain C: K.47, D.76, D.95 Ligands: POP.11 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.76, C:D.95 MG.16: 6 residues within 4Å: Chain D: K.47, N.75, D.76, G.92, D.95 Ligands: POP.15 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.76, D:D.95 MG.20: 5 residues within 4Å: Chain E: K.47, N.75, D.76, D.95 Ligands: POP.19 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.76, E:D.95 MG.24: 4 residues within 4Å: Chain F: K.47, D.76, D.95 Ligands: POP.23 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:D.76, F:D.95

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Paul, D. et al., Domain Organization in Candida glabrata THI6, a Bifunctional Enzyme Required for Thiamin Biosynthesis in Eukaryotes . Biochemistry (2010)

Release Date

2010-11-10

Peptides

Thiamine biosynthetic bifunctional enzyme: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Thiamine biosynthetic bifunctional enzyme