SMTL ID : 3nl6.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.61 Å

Oligo State

homo-hexamer

Ligands

6 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.1: 3 residues within 4Å: Chain A: D.340, E.372 Ligands: ACP.3 No protein-ligand interaction detected (PLIP) MG.4: 1 residues within 4Å: Ligands: ACP.6 No protein-ligand interaction detected (PLIP) MG.7: 4 residues within 4Å: Chain C: D.340, V.342, C.466 Ligands: ACP.9 No protein-ligand interaction detected (PLIP) MG.10: 3 residues within 4Å: Chain D: D.340, E.372 Ligands: ACP.12 No protein-ligand interaction detected (PLIP) MG.13: 1 residues within 4Å: Ligands: ACP.15 No protein-ligand interaction detected (PLIP) MG.16: 4 residues within 4Å: Chain F: D.340, V.342, C.466 Ligands: ACP.18 No protein-ligand interaction detected (PLIP)

6 x TPS: THIAMIN PHOSPHATE(Non-covalent)(Covalent)

TPS.2: 16 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.181, V.208, V.209, S.210 13 PLIP interactions: 13 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:G.181, A:V.209, A:S.210 pi-Stacking: A:H.90 TPS.5: 16 residues within 4Å: Chain B: 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, V.208, V.209, S.210 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:Y.13, B:Y.134, B:T.143, B:T.145, B:I.179 Hydrogen bonds: B:Q.43, B:Q.43, B:T.145, B:T.145, B:G.181, B:V.209, B:S.210 pi-Cation interactions: B:H.90 TPS.8: 16 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.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 Hydrogen bonds: C:Q.43, C:Q.43, C:T.143, C:T.145, C:T.145, C:G.181, C:L.182, C:V.209, C:S.210 pi-Cation interactions: C:H.90 TPS.11: 16 residues within 4Å: Chain D: 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.181, V.208, V.209, S.210 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:Y.13, D:Y.134, D:T.145, D:I.179, D:V.209 Hydrogen bonds: D:Q.43, D:Q.43, D:T.143, D:G.181, D:V.209, D:S.210 pi-Stacking: D:H.90 TPS.14: 16 residues within 4Å: Chain E: 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, V.208, V.209, S.210 14 PLIP interactions: 14 interactions with chain E Hydrophobic interactions: E:Y.13, E:Y.134, E:T.143, E:T.145, E:I.179 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-Cation interactions: E:H.90 TPS.17: 16 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.181, V.208, V.209, S.210 11 PLIP interactions: 11 interactions with chain F Hydrophobic interactions: F:Y.13, F:T.145, F:I.179 Hydrogen bonds: F:Q.43, F:Q.43, F:T.145, F:G.181, F:L.182, F:V.209, F:S.210 pi-Cation interactions: F:H.90

6 x ACP: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER(Non-covalent)(Covalent)

ACP.3: 18 residues within 4Å: Chain A: K.367, N.369, T.416, G.417, E.418, D.420, G.453, P.454, I.455, M.458, A.463, S.464, G.465, C.466, L.468, Y.496, K.497 Ligands: MG.1 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:K.367, A:N.369, A:T.416, A:E.418, A:E.418, A:D.420, A:I.455, A:A.463, A:S.464, A:S.464, A:G.465, A:C.466, A:K.497 ACP.6: 16 residues within 4Å: Chain B: N.369, T.416, G.417, E.418, D.420, G.453, I.455, M.458, A.463, S.464, G.465, C.466, L.468, Y.496, K.497 Ligands: MG.4 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:N.369, B:G.417, B:D.420, B:I.455, B:A.463, B:S.464, B:G.465, B:K.497 Salt bridges: B:K.367 ACP.9: 18 residues within 4Å: Chain C: N.369, E.372, T.416, G.417, E.418, D.420, G.453, P.454, I.455, M.458, I.461, A.463, S.464, G.465, C.466, L.468, K.497 Ligands: MG.7 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:N.369, C:T.416, C:G.417, C:E.418, C:E.418, C:D.420, C:I.455, C:A.463, C:S.464, C:S.464, C:G.465 ACP.12: 18 residues within 4Å: Chain D: K.367, N.369, T.416, G.417, E.418, D.420, G.453, P.454, I.455, M.458, A.463, S.464, G.465, C.466, L.468, Y.496, K.497 Ligands: MG.10 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:K.367, D:N.369, D:E.418, D:D.420, D:I.455, D:A.463, D:S.464, D:S.464, D:G.465, D:C.466, D:K.497 ACP.15: 16 residues within 4Å: Chain E: N.369, T.416, G.417, E.418, D.420, G.453, I.455, M.458, A.463, S.464, G.465, C.466, L.468, Y.496, K.497 Ligands: MG.13 9 PLIP interactions: 9 interactions with chain E Hydrogen bonds: E:N.369, E:G.417, E:D.420, E:I.455, E:A.463, E:S.464, E:G.465, E:K.497 Salt bridges: E:K.367 ACP.18: 18 residues within 4Å: Chain F: N.369, E.372, T.416, G.417, E.418, D.420, G.453, P.454, I.455, M.458, I.461, A.463, S.464, G.465, C.466, L.468, K.497 Ligands: MG.16 11 PLIP interactions: 11 interactions with chain F Hydrogen bonds: F:N.369, F:T.416, F:T.416, F:G.417, F:E.418, F:D.420, F:I.455, F:A.463, F:S.464, F:S.464, F:G.465

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
A

E
B

F
C

Thiamine biosynthetic bifunctional enzyme

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