Structure of PDB 2r8o Chain B Binding Site BS01

Receptor Information
>2r8o Chain B (length=667) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SSRKELANAIRALSMDAVQKAKSGHPGAPMGMADIAEVLWRDFLKHNPQN
PSWADRDRFVLSNGHGSMLIYSLLHLTGYDLPMEELKNFRQLHSKTPGHP
EVGYTAGVETTTGPLGQGIANAVGMAIAEKTLAAQFNRPGHDIVDHYTYA
FMGDGCMMEGISHEVCSLAGTLKLGKLIAFYDDNGISIDGHVEGWFTDDT
AMRFEAYGWHVIRDIDGHDAASIKRAVEEARAVTDKPSLLMCKTIIGFGS
PNKAGTHDSHGAPLGDAEIALTREQLGWKYAPFEIPSEIYAQWDAKEAGQ
AKESAWNEKFAAYAKAYPQEAAEFTRRMKGEMPSDFDAKAKEFIAKLQAN
PAKIASRKASQNAIEAFGPLLPEFLGGSADLAPSNLTLWSGSKAINEDAA
GNYIHYGVREFGMTAIANGISLHGGFLPYTSTFLMFVEYARNAVRMAALM
KQRQVMVYTHDSIGLGEDGPTHQPVEQVASLRVTPNMSTWRPCDQVESAV
AWKYGVERQDGPTALILSRQNLAQQERTEEQLANIARGGYVLKDCAGQPE
LIFIATGSEVELAVAAYEKLTAEGVKARVVSMPSTDAFDKQDAAYRESVL
PKAVTARVAVEAGIADYWYKYVGLNGAIVGMTTFGESAPAELLFEEFGFT
VDNVVAKAKELLHHHHH
Ligand information
Ligand IDT5X
InChIInChI=1S/C17H29N4O15P3S/c1-9-13(3-4-34-39(32,33)36-38(29,30)31)40-16(21(9)6-11-5-19-10(2)20-15(11)18)17(25,8-22)14(24)12(23)7-35-37(26,27)28/h5,12,14,22-25H,3-4,6-8H2,1-2H3,(H6-,18,19,20,26,27,28,29,30,31,32,33)/p+1/t12-,14+,17+/m1/s1
InChIKeyCRLXIEJPMQNLRP-IFIJOSMWSA-O
SMILES
SoftwareSMILES
ACDLabs 10.04O=P(O)(O)OCC(O)C(O)C(O)(c1sc(c([n+]1Cc2cnc(nc2N)C)C)CCOP(=O)(O)OP(=O)(O)O)CO
CACTVS 3.341Cc1ncc(C[n+]2c(C)c(CCO[P@](O)(=O)O[P](O)(O)=O)sc2[C@](O)(CO)[C@@H](O)[C@H](O)CO[P](O)(O)=O)c(N)n1
CACTVS 3.341Cc1ncc(C[n+]2c(C)c(CCO[P](O)(=O)O[P](O)(O)=O)sc2[C](O)(CO)[CH](O)[CH](O)CO[P](O)(O)=O)c(N)n1
OpenEye OEToolkits 1.5.0Cc1c(sc([n+]1Cc2cnc(nc2N)C)C(CO)(C(C(COP(=O)(O)O)O)O)O)CCOP(=O)(O)OP(=O)(O)O
OpenEye OEToolkits 1.5.0Cc1c(sc([n+]1Cc2cnc(nc2N)C)[C@](CO)([C@H]([C@@H](COP(=O)(O)O)O)O)O)CCO[P@@](=O)(O)OP(=O)(O)O
FormulaC17 H30 N4 O15 P3 S
Name2-C-{3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1,3-thia zol-3-ium-2-yl}-5-O-phosphono-D-xylitol;
D-XYLULOSE-5-PHOSPHATE THIAMIN DIPHOSPHATE ADDUCT
ChEMBL
DrugBank
ZINCZINC000024933683
PDB chain2r8o Chain A Residue 671 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB2r8o Strain and near attack conformers in enzymic thiamin catalysis: X-ray crystallographic snapshots of bacterial transketolase in covalent complex with donor ketoses xylulose 5-phosphate and fructose 6-phosphate, and in noncovalent complex with acceptor aldose ribose 5-phosphate.
Resolution1.47 Å
Binding residue
(original residue number in PDB)		D381 S385 E411 F434 F437 Y440 H461 D469 H473 R520
Binding residue
(residue number reindexed from 1)		D380 S384 E410 F433 F436 Y439 H460 D468 H472 R519
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) H26 I247 H261 E411 H473
Catalytic site (residue number reindexed from 1) H25 I246 H260 E410 H472
Enzyme Commision number 2.2.1.1: transketolase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0003824 catalytic activity
GO:0004802 transketolase activity
GO:0016740 transferase activity
GO:0030145 manganese ion binding
GO:0030976 thiamine pyrophosphate binding
GO:0042803 protein homodimerization activity
GO:0046872 metal ion binding
Biological Process
GO:0006098 pentose-phosphate shunt
GO:0009052 pentose-phosphate shunt, non-oxidative branch
Cellular Component
GO:0005829 cytosol

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:2r8o, PDBe:2r8o, PDBj:2r8o
PDBsum2r8o
PubMed17914867
UniProtP27302|TKT1_ECOLI Transketolase 1 (Gene Name=tktA)

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