SMTL ID : 3nl3.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.01 Å

Oligo State

homo-hexamer

Ligands

6 x TPS: THIAMIN PHOSPHATE(Non-covalent)

TPS.1: 17 residues within 4Å: Chain A: Y.13, Q.43, R.45, N.75, H.90, S.114, Y.134, G.136, T.139, T.143, T.145, I.179, G.180, G.181, V.208, V.209, S.210 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:Y.13, A:Y.134, A:T.145, A:I.179, A:V.209 Hydrogen bonds: A:Q.43, A:Q.43, A:T.143, A:T.145, A:T.145, A:G.181, A:V.209, A:S.210 pi-Stacking: A:H.90 TPS.5: 18 residues within 4Å: Chain B: Y.13, Q.43, R.45, N.75, H.90, S.114, Y.134, G.136, T.139, T.143, T.145, K.146, I.179, G.180, G.181, V.208, V.209, S.210 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:Y.13, B:Y.134, B:T.145, B:I.179 Hydrogen bonds: B:Q.43, B:Q.43, B:T.145, B:G.181, B:V.209, B:S.210 pi-Stacking: B:H.90 TPS.7: 17 residues within 4Å: Chain C: Y.13, Q.43, R.45, N.75, H.90, S.114, Y.134, G.136, T.139, T.143, T.145, I.179, G.180, G.181, V.208, V.209, S.210 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:Y.13, C:T.145, C:I.179, C:V.209 Hydrogen bonds: C:Q.43, C:Q.43, C:T.143, C:T.145, C:T.145, C:G.181, C:V.209, C:S.210 pi-Stacking: C:H.90 TPS.10: 17 residues within 4Å: Chain D: Y.13, Q.43, R.45, H.90, S.114, Y.134, G.136, T.139, T.143, T.145, I.179, G.180, G.181, C.207, V.208, V.209, S.210 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:Y.13, D:Y.134, D:I.179, D:V.209 Hydrogen bonds: D:Q.43, D:Q.43, D:T.145, D:G.181, D:V.209, D:S.210 pi-Stacking: D:H.90 TPS.14: 18 residues within 4Å: Chain E: Y.13, Q.43, R.45, N.75, H.90, S.114, Y.134, G.136, T.139, T.143, T.145, K.146, I.179, G.180, G.181, V.208, V.209, S.210 11 PLIP interactions: 11 interactions with chain E Hydrophobic interactions: E:Y.13, E:T.145 Hydrogen bonds: E:Q.43, E:Q.43, E:T.143, E:T.145, E:T.145, E:G.181, E:V.209, E:S.210 pi-Stacking: E:H.90 TPS.16: 17 residues within 4Å: Chain F: Y.13, Q.43, R.45, N.75, H.90, S.114, Y.134, G.136, T.139, T.143, T.145, I.179, G.180, G.181, V.208, V.209, S.210 13 PLIP interactions: 13 interactions with chain F Hydrophobic interactions: F:Y.13, F:Y.134, F:T.145, F:I.179, F:V.209 Hydrogen bonds: F:Q.43, F:Q.43, F:T.143, F:T.145, F:G.181, F:L.182, F:V.209, F:S.210

12 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: D.76, D.95 Chain C: T.51 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Metal complexes: A:D.76, A:D.95, C:T.51 MG.3: 6 residues within 4Å: Chain A: L.241, T.243, D.424, T.426, I.427, E.428 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.424 MG.4: 3 residues within 4Å: Chain A: D.340, P.341, E.372 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:P.341, A:E.372, A:E.372 MG.6: 3 residues within 4Å: Chain B: D.340, P.341, E.372 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:P.341, B:E.372, B:E.372 MG.8: 3 residues within 4Å: Chain A: T.51 Chain C: D.76, D.95 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.51 MG.9: 3 residues within 4Å: Chain C: D.340, P.341, E.372 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.340, C:P.341, C:E.372, C:E.372 MG.11: 3 residues within 4Å: Chain D: D.76, D.95 Chain E: T.51 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain D Metal complexes: E:T.51, D:D.76 MG.12: 5 residues within 4Å: Chain D: A.49, D.50, T.51 Chain E: D.76, D.95 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain E Metal complexes: D:A.49, D:T.51, E:D.76 MG.13: 3 residues within 4Å: Chain D: D.340, P.341, E.372 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:P.341, D:E.372, D:E.372 MG.15: 3 residues within 4Å: Chain E: D.340, P.341, E.372 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:P.341, E:E.372, E:E.372 MG.17: 3 residues within 4Å: Chain B: T.51 Chain F: D.76, D.95 3 PLIP interactions: 2 interactions with chain F, 1 interactions with chain B Metal complexes: F:D.76, F:D.95, B:T.51 MG.18: 3 residues within 4Å: Chain F: D.340, P.341, E.372 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:P.341, F:E.372, F:E.372

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

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