Structure of PDB 1pvy Chain A Binding Site BS01

Receptor Information
>1pvy Chain A (length=219) Species: 2190 (Methanocaldococcus jannaschii) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NNVEKAIEALKKGEIILVYDSDEREGETDMVVASQFITPEHIRIMRKDAG
GLICTALHPDICNKLGIPFMVDILEFASQKFKVLRELYPNDIPYDEKSSF
SITINHRKTFTGITDNDRAFTIKKLAELVKEGRFNDFGKEFRSPGSVTLL
RAAEGLVKNRQGHTEMTVALAELANLVPITTICEMMGDDGNAMSKNETKR
YAEKHNLIYLSGEEIINYY
Ligand information
Ligand ID5RP
InChIInChI=1S/C5H11O8P/c6-1-3(7)5(9)4(8)2-13-14(10,11)12/h4-6,8-9H,1-2H2,(H2,10,11,12)/t4-,5+/m1/s1
InChIKeyFNZLKVNUWIIPSJ-UHNVWZDZSA-N
SMILES
SoftwareSMILES
CACTVS 3.341OCC(=O)[C@H](O)[C@H](O)CO[P](O)(O)=O
OpenEye OEToolkits 1.5.0C(C(C(C(=O)CO)O)O)OP(=O)(O)O
CACTVS 3.341OCC(=O)[CH](O)[CH](O)CO[P](O)(O)=O
ACDLabs 10.04O=P(O)(O)OCC(O)C(O)C(=O)CO
OpenEye OEToolkits 1.5.0C([C@H]([C@H](C(=O)CO)O)O)OP(=O)(O)O
FormulaC5 H11 O8 P
NameRIBULOSE-5-PHOSPHATE
ChEMBL
DrugBank
ZINCZINC000001532567
PDB chain1pvy Chain A Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1pvy Structure of 3,4-Dihydroxy-2-butanone 4-Phosphate Synthase from Methanococcus jannaschii in Complex with Divalent Metal Ions and the Substrate Ribulose 5-Phosphate: IMPLICATIONS FOR THE CATALYTIC MECHANISM
Resolution1.7 Å
Binding residue
(original residue number in PDB)		R25 E26 D30 C55 L151 R161 G163 H164 T165 I183 E185
Binding residue
(residue number reindexed from 1)		R24 E25 D29 C54 L150 R160 G162 H163 T164 I182 E184
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) E26 D30 C55 Y95 F101 N106 S147 H164 E185
Catalytic site (residue number reindexed from 1) E25 D29 C54 Y94 F100 N105 S146 H163 E184
Enzyme Commision number 4.1.99.12: 3,4-dihydroxy-2-butanone-4-phosphate synthase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0003824 catalytic activity
GO:0008686 3,4-dihydroxy-2-butanone-4-phosphate synthase activity
GO:0016829 lyase activity
GO:0030145 manganese ion binding
GO:0046872 metal ion binding
Biological Process
GO:0009231 riboflavin biosynthetic process
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:1pvy, PDBe:1pvy, PDBj:1pvy
PDBsum1pvy
PubMed12904291
UniProtQ60364|RIBB_METJA 3,4-dihydroxy-2-butanone 4-phosphate synthase (Gene Name=ribB)

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