Structure of PDB 5nv3 Chain D Binding Site BS03

Receptor Information
>5nv3 Chain D (length=467) Species: 1063 (Cereibacter sphaeroides) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RYKAGVLKYAQMGYWDGDYVPKDTDVLALFRITPQEGVDPVEAAAAVAGE
SSTATWTVVWTDRLTACDSYRAKAYRVEPVPGTPGQYFCYVAYDLILFEE
GSIANLTASIIGNVFSFKPLKAARLEDMRFPVAYVKTYKGPPTGIVGERE
RLDKFGKPLLGATTKPKLGLSGKNYGRVVYEGLKGGLDFMKDDENINSQP
FMHWRDRFLYVMEAVNLASAQTGEVKGHYLNITAGTMEEMYRRAEFAKSL
GSVIVMVDLIIGYTAIQSISEWCRQNDMILHMHRAGHGTYTRQKNHGISF
RVIAKWLRLAGVDHLHCGTAVGKLEGDPLTVQGYYNVCREPFNTVDLPRG
IFFEQDWADLRKVMPVASGGIHAGQMHQLLSLFGDDVVLQFGGGTIGHPM
GIQAGATANRVALEAMVLARNEGRNIDVEGPEILRAAAKWCKPLEAALDT
WGNITFNYTSTDTSDFV
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 chain5nv3 Chain H Residue 1001 [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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PDB5nv3 Mechanism of Enzyme Repair by the AAA(+) Chaperone Rubisco Activase.
Resolution3.39 Å
Binding residue
(original residue number in PDB)		E62 W68 N125
Binding residue
(residue number reindexed from 1)		E50 W56 N113
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) D205 E206 H295 H328 K335
Catalytic site (residue number reindexed from 1) D193 E194 H283 H316 K323
Enzyme Commision number 4.1.1.39: ribulose-bisphosphate carboxylase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0004497 monooxygenase activity
GO:0016829 lyase activity
GO:0016984 ribulose-bisphosphate carboxylase activity
GO:0046872 metal ion binding
Biological Process
GO:0015977 carbon fixation
GO:0015979 photosynthesis
GO:0019253 reductive pentose-phosphate cycle

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5nv3, PDBe:5nv3, PDBj:5nv3
PDBsum5nv3
PubMed28803776
UniProtP27997|RBL1_CERSP Ribulose bisphosphate carboxylase large chain (Gene Name=cbbL)

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