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EBI Groups Thornton CoFactor

Conformations of Thiamine diphosphate in protein structures

Below you will find a JMOL applet of the superimosed molecules of Thiamine diphosphate. There is one applet for each PDB HET code that is associated with this cofactor. The structures have been clustered by their pairwise distance (RMSD) and each cluster has a different colour. The clustering algorithm is described in reference [KGS].

These applets illustrate the conformational space that the cofactor has when bound to the protein. The superposition has been performed on the most rigid part (aromatic ring structures where possible). This information is even more useful when combined with the solvent accessibility analysis.

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Structures for HET code TDP

Structure Cluster Species E.C. number CATH domain Resolution
1u5b Homo sapiens
(Human)		 1.2.4.4 3.40.50.970 1.83Å
3k95 N/A 2.2.1.1 3.40.50.970 2.00Å
2bfe Homo sapiens
(Human)		 1.2.4.4 3.40.50.970 1.69Å
2bfb Homo sapiens
(Human)		 1.2.4.4 3.40.50.970 1.77Å
1x80 Homo sapiens
(Human)		 1.2.4.4 3.40.50.970 2.00Å
1x7z Homo sapiens
(Human)		 1.2.4.4 3.40.50.970 1.72Å
1x7y Homo sapiens
(Human)		 1.2.4.4 3.40.50.970 1.57Å
1x7w Homo sapiens
(Human)		 1.2.4.4 3.40.50.970 1.73Å
2bfd Homo sapiens
(Human)		 1.2.4.4 3.40.50.970 1.39Å
1v11 Homo sapiens
(Human)		 1.2.4.4 3.40.50.970 1.95Å
1v1m Homo sapiens
(Human)		 1.2.4.4 3.40.50.970 2.00Å
1x7x Homo sapiens
(Human)		 1.2.4.4 3.40.50.970 2.10Å
1v16 Homo sapiens
(Human)		 1.2.4.4 3.40.50.970 1.90Å
1w85 Geobacillus stearothermophilus
(Bacillus stearothermophilus)		 2.3.1.12 3.40.50.970 2.00Å
1dtw Homo sapiens
(Human)		 1.2.4.4 3.40.50.970 2.70Å
1olx Homo sapiens
(Human)		 1.2.4.4 3.40.50.970 2.25Å
1olu Homo sapiens
(Human)		 1.2.4.4 3.40.50.970 1.90Å
1umd Thermus thermophilus
(strain HB8 / ATCC 27634 / DSM 579)		 1.2.4.4 3.40.50.970 1.90Å
1umc Thermus thermophilus
(strain HB8 / ATCC 27634 / DSM 579)		 1.2.4.4 3.40.50.970 2.40Å
1umb Thermus thermophilus
(strain HB8 / ATCC 27634 / DSM 579)		 1.2.4.4 3.40.50.970 2.10Å
1qs0 Pseudomonas putida 1.2.4.4 3.40.50.970 2.40Å
1pyd Saccharomyces cerevisiae
(Baker's yeast)		 4.1.1.1 3.40.50.970 2.40Å
1w88 N/A 2.3.1.12 3.40.50.970 2.30Å
1l8a Escherichia coli
(strain K12)		 1.2.4.1 1.85Å
2iea Escherichia coli
(strain K12)		 1.2.4.1 1.85Å
2qta Escherichia coli
(strain K12)		 1.2.4.1 1.85Å
1mcz Pseudomonas putida 4.1.1.7 3.40.50.970 2.80Å
2o1s Escherichia coli
(strain K12)		 2.2.1.7 2.40Å
3ey9 Escherichia coli
(strain K12)		 1.2.2.2 2.90Å
2fwn Pseudomonas putida 4.1.1.7 3.40.50.1220 1.40Å
2o1x Deinococcus radiodurans 2.2.1.7 2.90Å
2pan Escherichia coli
(strain K12)		 4.1.1.47 2.70Å
3eya Escherichia coli
(strain K12)		 1.2.2.2 2.50Å

Structures for HET code TPP

Structure Cluster Species E.C. number CATH domain Resolution
1jsc Saccharomyces cerevisiae
(Baker's yeast)		 2.2.1.6 3.40.50.970 2.60Å
2ji8 Oxalobacter formigenes 4.1.1.8 2.15Å
2ag0 Pseudomonas fluorescens 2.58Å
2pgo N/A 1.26Å
2w93 Saccharomyces cerevisiae
(Baker's yeast)		 4.1.1.1 3.40.50.1220 1.60Å
2vk8 Saccharomyces cerevisiae
(Baker's yeast)		 4.1.1.1 1.42Å
2vk1 Saccharomyces cerevisiae
(Baker's yeast)		 4.1.1.1 1.71Å
2vjy Kluyveromyces lactis
(Yeast)
(Candida sphaerica)		 4.1.1.1 2.30Å
1z8n Arabidopsis thaliana
(Mouse-ear cress)		 2.2.1.6 2.80Å
1v5f N/A 1.2.3.3 1.80Å
1ay0 Saccharomyces cerevisiae
(Baker's yeast)		 2.2.1.1 3.40.50.970 2.60Å
1pox Lactobacillus plantarum 1.2.3.3 3.40.50.970 2.10Å
3c9u Aquifex aeolicus 3.90.650.10 1.48Å
2c3o Desulfovibrio africanus 2.70Å
1b0p Desulfovibrio africanus 2.31Å
3exf Homo sapiens
(Human)		 1.2.4.1 3.00Å
2pda Desulfovibrio africanus 4.10.790.10 3.00Å
2v3w Pseudomonas putida 4.1.1.7 2.20Å
2nxw Azospirillum brasilense 4.1.1.74 1.50Å
3exh Homo sapiens
(Human)		 1.2.4.1 2.44Å
1r9j Leishmania mexicana mexicana 2.2.1.1 2.22Å
2vbf Lactococcus lactis 1.60Å
1trk Saccharomyces cerevisiae
(Baker's yeast)		 2.2.1.1 3.40.50.970 2.00Å
1pow Lactobacillus plantarum 1.2.3.3 3.40.50.970 2.50Å
3exe Homo sapiens
(Human)		 1.2.4.1 1.98Å
2r5n Escherichia coli
(strain K12)		 2.2.1.1 1.60Å
2ez4 Lactobacillus plantarum 1.2.3.3 3.40.50.970 2.03Å
2pgn N/A 1.20Å
2ag1 Pseudomonas fluorescens 2.58Å
1ovm Enterobacter cloacae 4.1.1.74 3.40.50.970 2.65Å
1y9d Lactobacillus plantarum 1.2.3.3 3.40.50.970 2.20Å
2jib Oxalobacter formigenes 4.1.1.8 2.20Å
2c42 Desulfovibrio africanus 1.78Å
2vk4 Kluyveromyces lactis
(Yeast)
(Candida sphaerica)		 4.1.1.1 1.95Å
1pvd Saccharomyces cerevisiae
(Baker's yeast)		 4.1.1.1 3.40.50.970 2.30Å
1ngs Saccharomyces cerevisiae
(Baker's yeast)		 2.2.1.1 3.40.50.970 2.40Å
1n0h Saccharomyces cerevisiae
(Baker's yeast)		 2.2.1.6 2.80Å
1ni4 Homo sapiens
(Human)		 1.2.4.1 3.40.50.970 1.95Å
1itz Zea mays
(Maize)		 2.2.1.1 3.40.50.970 2.30Å
2uz1 Pseudomonas fluorescens 1.65Å
2c3m Desulfovibrio africanus 1.84Å
1qgd Escherichia coli
(strain K12)		 2.2.1.1 3.40.50.970 1.90Å
1bfd Pseudomonas putida 4.1.1.7 3.40.50.970 1.60Å
2vbi Acetobacter pasteurianus
(Acetobacter turbidans)		 4.1.1.1 2.75Å
2ozl Homo sapiens
(Human)		 1.2.4.1 1.90Å
1ozf Klebsiella pneumoniae 2.2.1.6 3.40.50.970 2.30Å
1upa Streptomyces clavuligerus 2.35Å
1upb Streptomyces clavuligerus 2.35Å
1upc Streptomyces clavuligerus 2.45Å
2cky N/A 2.90Å
2gdi N/A 2.05Å
3d2g N/A 2.25Å
2hoj N/A 2.50Å
2hok N/A 3.20Å
2hol N/A 2.90Å
3e78 Mycoplasma hyorhinis 1.90Å
3e79 Mycoplasma hyorhinis 1.90Å
3eki Mycoplasma hyorhinis 1.60Å

References

[KGS] pubmed:8961360
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