SMTL ID : 1rp0.1

Crystal Structure of Thi1 protein from Arabidopsis thaliana

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-octamer

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 3 residues within 4Å: Chain A: H.189, D.190 Ligands: AHZ.2 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.189, A:D.190, H2O.9, H2O.9 ZN.4: 3 residues within 4Å: Chain B: H.189, D.190 Ligands: AHZ.5 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.189, B:D.190, H2O.17, H2O.17 ZN.6: 3 residues within 4Å: Chain C: H.189, D.190 Ligands: AHZ.7 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:H.189, C:D.190, H2O.25, H2O.25 ZN.9: 3 residues within 4Å: Chain D: H.189, D.190 Ligands: AHZ.10 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:H.189, D:D.190, H2O.34, H2O.34 ZN.11: 3 residues within 4Å: Chain E: H.189, D.190 Ligands: AHZ.12 4 PLIP interactions: 2 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:H.189, E:D.190, H2O.42, H2O.42 ZN.14: 3 residues within 4Å: Chain F: H.189, D.190 Ligands: AHZ.15 4 PLIP interactions: 2 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:H.189, F:D.190, H2O.51, H2O.51 ZN.16: 3 residues within 4Å: Chain G: H.189, D.190 Ligands: AHZ.17 4 PLIP interactions: 2 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:H.189, G:D.190, H2O.59, H2O.59 ZN.19: 3 residues within 4Å: Chain H: H.189, D.190 Ligands: AHZ.20 4 PLIP interactions: 2 interactions with chain H, 2 Ligand-Water interactions Metal complexes: H:H.189, H:D.190, H2O.68, H2O.68

8 x AHZ: ADENOSINE DIPHOSPHATE 5-(BETA-ETHYL)-4-METHYL-THIAZOLE-2-CARBOXYLIC ACID(Non-covalent)

AHZ.2: 31 residues within 4Å: Chain A: V.45, G.46, A.47, G.48, S.49, A.50, I.69, E.70, Q.71, G.77, G.78, V.141, A.142, A.143, S.186, C.187, G.188, H.189, D.190, F.193, T.196, G.240, M.241, R.251, M.252, G.253, M.259 Chain D: C.172, D.174, P.175 Ligands: ZN.1 30 PLIP interactions: 28 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:A.50, A:Q.71, A:Q.71, A:G.77, A:G.78, A:A.143, A:G.188, A:T.196, A:T.196, A:M.241, A:M.252, A:G.253 Water bridges: A:G.48, A:G.48, A:S.49, A:S.49, A:E.70, A:E.70, A:S.72, A:G.77, A:S.186, A:H.189, A:D.190, A:E.242, A:R.251, A:R.251, D:D.174, D:D.174 Salt bridges: A:H.189, A:R.251 AHZ.5: 29 residues within 4Å: Chain B: V.45, G.46, G.48, S.49, A.50, I.69, E.70, Q.71, G.77, G.78, V.141, A.142, A.143, S.186, C.187, G.188, H.189, D.190, F.193, T.196, G.240, M.241, R.251, M.252, G.253, M.259 Chain G: C.172, D.174 Ligands: ZN.4 27 PLIP interactions: 27 interactions with chain B Hydrogen bonds: B:A.50, B:Q.71, B:G.77, B:G.78, B:A.143, B:G.188, B:T.196, B:T.196, B:M.241, B:M.252, B:G.253 Water bridges: B:G.48, B:S.49, B:S.49, B:G.51, B:E.70, B:E.70, B:E.70, B:Q.71, B:S.186, B:H.189, B:D.190, B:D.190, B:E.242, B:R.251 Salt bridges: B:H.189, B:R.251 AHZ.7: 31 residues within 4Å: Chain B: C.172, D.174, P.175 Chain C: V.45, G.46, A.47, G.48, S.49, A.50, I.69, E.70, Q.71, G.77, G.78, V.141, A.142, A.143, S.186, C.187, G.188, H.189, D.190, F.193, T.196, G.240, M.241, R.251, M.252, G.253, M.259 Ligands: ZN.6 28 PLIP interactions: 28 interactions with chain C Hydrogen bonds: C:A.50, C:Q.71, C:Q.71, C:G.77, C:G.78, C:A.143, C:G.188, C:T.196, C:T.196, C:M.241, C:M.252, C:G.253 Water bridges: C:G.48, C:G.48, C:S.49, C:S.49, C:E.70, C:E.70, C:S.72, C:G.77, C:S.186, C:H.189, C:D.190, C:E.242, C:R.251, C:R.251 Salt bridges: C:H.189, C:R.251 AHZ.10: 29 residues within 4Å: Chain D: V.45, G.46, G.48, S.49, A.50, I.69, E.70, Q.71, G.77, G.78, V.141, A.142, A.143, S.186, C.187, G.188, H.189, D.190, F.193, T.196, G.240, M.241, R.251, M.252, G.253, M.259 Chain E: C.172, D.174 Ligands: ZN.9 29 PLIP interactions: 27 interactions with chain D, 2 interactions with chain E Hydrogen bonds: D:A.50, D:Q.71, D:G.77, D:G.78, D:A.143, D:G.188, D:T.196, D:T.196, D:M.241, D:M.252, D:G.253 Water bridges: D:G.48, D:S.49, D:S.49, D:G.51, D:E.70, D:E.70, D:E.70, D:Q.71, D:S.186, D:H.189, D:D.190, D:D.190, D:E.242, D:R.251, E:D.174, E:D.174 Salt bridges: D:H.189, D:R.251 AHZ.12: 31 residues within 4Å: Chain E: V.45, G.46, A.47, G.48, S.49, A.50, I.69, E.70, Q.71, G.77, G.78, V.141, A.142, A.143, S.186, C.187, G.188, H.189, D.190, F.193, T.196, G.240, M.241, R.251, M.252, G.253, M.259 Chain H: C.172, D.174, P.175 Ligands: ZN.11 28 PLIP interactions: 28 interactions with chain E Hydrogen bonds: E:A.50, E:Q.71, E:Q.71, E:G.77, E:G.78, E:A.143, E:G.188, E:T.196, E:T.196, E:M.241, E:M.252, E:G.253 Water bridges: E:G.48, E:G.48, E:S.49, E:S.49, E:E.70, E:E.70, E:S.72, E:G.77, E:S.186, E:H.189, E:D.190, E:E.242, E:R.251, E:R.251 Salt bridges: E:H.189, E:R.251 AHZ.15: 29 residues within 4Å: Chain C: C.172, D.174 Chain F: V.45, G.46, G.48, S.49, A.50, I.69, E.70, Q.71, G.77, G.78, V.141, A.142, A.143, S.186, C.187, G.188, H.189, D.190, F.193, T.196, G.240, M.241, R.251, M.252, G.253, M.259 Ligands: ZN.14 29 PLIP interactions: 27 interactions with chain F, 2 interactions with chain C Hydrogen bonds: F:A.50, F:Q.71, F:G.77, F:G.78, F:A.143, F:G.188, F:T.196, F:T.196, F:M.241, F:M.252, F:G.253 Water bridges: F:G.48, F:S.49, F:S.49, F:G.51, F:E.70, F:E.70, F:E.70, F:Q.71, F:S.186, F:H.189, F:D.190, F:D.190, F:E.242, F:R.251, C:D.174, C:D.174 Salt bridges: F:H.189, F:R.251 AHZ.17: 31 residues within 4Å: Chain F: C.172, D.174, P.175 Chain G: V.45, G.46, A.47, G.48, S.49, A.50, I.69, E.70, Q.71, G.77, G.78, V.141, A.142, A.143, S.186, C.187, G.188, H.189, D.190, F.193, T.196, G.240, M.241, R.251, M.252, G.253, M.259 Ligands: ZN.16 30 PLIP interactions: 28 interactions with chain G, 2 interactions with chain F Hydrogen bonds: G:A.50, G:Q.71, G:Q.71, G:G.77, G:G.78, G:A.143, G:G.188, G:T.196, G:T.196, G:M.241, G:M.252, G:G.253 Water bridges: G:G.48, G:G.48, G:S.49, G:S.49, G:E.70, G:E.70, G:S.72, G:G.77, G:S.186, G:H.189, G:D.190, G:E.242, G:R.251, G:R.251, F:D.174, F:D.174 Salt bridges: G:H.189, G:R.251 AHZ.20: 29 residues within 4Å: Chain A: C.172, D.174 Chain H: V.45, G.46, G.48, S.49, A.50, I.69, E.70, Q.71, G.77, G.78, V.141, A.142, A.143, S.186, C.187, G.188, H.189, D.190, F.193, T.196, G.240, M.241, R.251, M.252, G.253, M.259 Ligands: ZN.19 27 PLIP interactions: 27 interactions with chain H Hydrogen bonds: H:A.50, H:Q.71, H:G.77, H:G.78, H:A.143, H:G.188, H:T.196, H:T.196, H:M.241, H:M.252, H:G.253 Water bridges: H:G.48, H:S.49, H:S.49, H:G.51, H:E.70, H:E.70, H:E.70, H:Q.71, H:S.186, H:H.189, H:D.190, H:D.190, H:E.242, H:R.251 Salt bridges: H:H.189, H:R.251

4 x HTO: HEPTANE-1,2,3-TRIOL(Non-covalent)

HTO.3: 4 residues within 4Å: Chain A: D.110, T.111 Chain C: P.16, I.17 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:D.110, A:T.111, C:P.16 HTO.8: 4 residues within 4Å: Chain A: P.16, I.17 Chain C: D.110, T.111 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:D.110, C:T.111, A:P.16 HTO.13: 4 residues within 4Å: Chain E: D.110, T.111 Chain G: P.16, I.17 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain G Hydrophobic interactions: E:D.110, E:T.111, G:P.16 HTO.18: 4 residues within 4Å: Chain E: P.16, I.17 Chain G: D.110, T.111 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain G Hydrophobic interactions: E:P.16, G:D.110, G:T.111

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Godoi, P.H. et al., Structure of the thiazole biosynthetic enzyme THI1 from Arabidopsis thaliana. J.Biol.Chem. (2006)

Release Date

2005-02-22

Peptides

Thiazole biosynthetic enzyme: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

G
A

H
B

Thiazole biosynthetic enzyme