Structure of PDB 3kdn Chain A Binding Site BS02

Receptor Information
>3kdn Chain A (length=437) Species: 69014 (Thermococcus kodakarensis KOD1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IYDYYVDKGYEPSKKRDIIAVFRVTPAEGYTIEQAAGAVAAESSTGTWTT
LYPWYEQERWADLSAKAYDFHDMGDGSWIVRIAYPFHAFEEANLPGLLAS
IAGNIFGMKRVKGLRLEDLYFPEKLIREFDGPAFGIEGVRKMLEIKDRPI
YGVVPKPKVGYSPEEFEKLAYDLLSNGADYMKDDENLTSPWYNRFEERAE
IMAKIIDKVENETGEKKTWFANITADLLEMEQRLEVLADLGLKHAMVDVV
ITGWGALRYIRDLAADYGLAIHGHRAMHAAFTRNPYHGISMFVLAKLYRL
IGIDQLHVGTAGAGKLEGERDITIQNARILRESHYKPDENDVFHLEQKFY
SIKAAFPTSSGGLHPGNIQPVIEALGTDIVLQLGGGTLGHPDGPAAGARA
VRQAIDAIMQGIPLDEYAKTHKELARALEKWGHVTPV
Ligand information
Ligand IDCAP
InChIInChI=1S/C6H14O13P2/c7-3(1-18-20(12,13)14)4(8)6(11,5(9)10)2-19-21(15,16)17/h3-4,7-8,11H,1-2H2,(H,9,10)(H2,12,13,14)(H2,15,16,17)/t3-,4-,6-/m1/s1
InChIKeyITHCSGCUQDMYAI-ZMIZWQJLSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C(C(C(C(COP(=O)(O)O)(C(=O)O)O)O)O)OP(=O)(O)O
CACTVS 3.341O[CH](CO[P](O)(O)=O)[CH](O)[C](O)(CO[P](O)(O)=O)C(O)=O
ACDLabs 10.04O=P(O)(O)OCC(O)C(O)C(O)(C(=O)O)COP(=O)(O)O
OpenEye OEToolkits 1.5.0C([C@H]([C@H]([C@](COP(=O)(O)O)(C(=O)O)O)O)O)OP(=O)(O)O
CACTVS 3.341O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@](O)(CO[P](O)(O)=O)C(O)=O
FormulaC6 H14 O13 P2
Name2-CARBOXYARABINITOL-1,5-DIPHOSPHATE
ChEMBL
DrugBank
ZINC
PDB chain3kdn Chain A Residue 600 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3kdn Structure-based catalytic optimization of a type III Rubisco from a hyperthermophile
Resolution2.09 Å
Binding residue
(original residue number in PDB)		K163 K189 D191 E192 H281 R282 H314 K322 L323 S367 G368 Q389
Binding residue
(residue number reindexed from 1)		K156 K182 D184 E185 H274 R275 H307 K315 L316 S360 G361 Q382
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) K163 K189 D190 D191 E192 H281 H314 K322
Catalytic site (residue number reindexed from 1) K156 K182 D183 D184 E185 H274 H307 K315
Enzyme Commision number 4.1.1.39: ribulose-bisphosphate carboxylase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0016491 oxidoreductase activity
GO:0016829 lyase activity
GO:0016984 ribulose-bisphosphate carboxylase activity
GO:0046872 metal ion binding
Biological Process
GO:0006196 AMP catabolic process
GO:0015977 carbon fixation

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3kdn, PDBe:3kdn, PDBj:3kdn
PDBsum3kdn
PubMed20926376
UniProtO93627|RBL_THEKO Ribulose bisphosphate carboxylase (Gene Name=rbcL)

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