Structure of PDB 3pyb Chain A Binding Site BS01

Receptor Information
>3pyb Chain A (length=685) Species: 3702 (Arabidopsis thaliana) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NSNAFKEAVKSVKTILRNLTDGEITISAYDTAWVALIDAGDKTPAFPSAV
KWIAENQLSDGSWGDAYLFSYHDRLINTLACVVALRSWNLFPHQCNKGIT
FFRENIGKLEDENDEHMPIGFEVAFPSLLEIARGINIDVPYDSPVLKDIY
AKKELKLTRIPKEIMHKIPTTLLHSLEGMRDLDWEKLLKLQSQDGSFLFS
PSSTAFAFMQTRDSNCLEYLRNAVKRFNGGVPNVFPVDLFEHIWIVDRLQ
RLGISRYFEEEIKECLDYVHRYWTDNGICWARCSHVQDIDDTAMAFRLLR
QHGYQVSADVFKNFEKEGEFFCFVGQSNQAVTGMFNLYRASQLAFPREEI
LKNAKEFSYNYLLEKREREELIDKWIIMKDLPGEIGFALEIPWYASLPRV
ETRFYIDQYGGENDVWIGKTLYRMPYVNNNGYLELAKQDYNNCQAQHQLE
WDIFQKWYEENRLSEWGVRRSELLECYYLAAATIFESERSHERMVWAKSS
VLVKAISSSFGESSDSRRSFSDQFHEYIANAGSVQASRLAGVLIGTLNQM
SFDLFMSHGRDVNNLLYLSWGDWMEKWKLYGDEGEGELMVKMIILMKNND
LTNFFTHTHFVRLAEIINRICLPEKTIKSMEKEMGKMVELALSESDTFRD
VSITFLDVAKAFYYFALCGDHLQTHISKVLFQKVG
Ligand information
Ligand IDA3C
InChIInChI=1S/C19H37NO7P2/c1-15-7-8-17-18(2,3)10-6-11-19(17,4)16(15)9-12-20(5)13-14-26-29(24,25)27-28(21,22)23/h16-17H,1,6-14H2,2-5H3,(H,24,25)(H2,21,22,23)/t16-,17-,19+/m0/s1
InChIKeyZYKKZQANNLZNRN-JENIJYKNSA-N
SMILES
SoftwareSMILES
CACTVS 3.370CN(CCO[P](O)(=O)O[P](O)(O)=O)CC[C@H]1C(=C)CC[C@H]2C(C)(C)CCC[C@]12C
CACTVS 3.370CN(CCO[P](O)(=O)O[P](O)(O)=O)CC[CH]1C(=C)CC[CH]2C(C)(C)CCC[C]12C
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OCCN(C)CCC1C(=C)\CCC2C(CCCC12C)(C)C
OpenEye OEToolkits 1.7.0CC1(CCCC2(C1CCC(=C)C2CCN(C)CCOP(=O)(O)OP(=O)(O)O)C)C
OpenEye OEToolkits 1.7.0C[C@]12CCCC([C@@H]1CCC(=C)[C@@H]2CC[N@@](C)CCO[P@](=O)(O)OP(=O)(O)O)(C)C
FormulaC19 H37 N O7 P2
Name2-(methyl{2-[(1S,4aS,8aS)-5,5,8a-trimethyl-2-methylidenedecahydronaphthalen-1-yl]ethyl}amino)ethyl trihydrogen diphosphate;
13-aza-13,14-dihydrocopalyl diphosphate
ChEMBL
DrugBank
ZINCZINC000058661288
PDB chain3pyb Chain A Residue 901 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3pyb Structure of ent-Copalyl Diphosphate Synthase from Arabidopsis thaliana, a Protonation-Dependent Diterpene Cyclase
Resolution2.759 Å
Binding residue
(original residue number in PDB)		Q791 S795 F799
Binding residue
(residue number reindexed from 1)		Q673 S677 F681
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) R559 L568 S589 S596 G600 G690 R725 L728 A784 D788
Catalytic site (residue number reindexed from 1) R470 L479 S500 S507 G511 G584 R619 L622 A666 D670
Enzyme Commision number 5.5.1.13: ent-copalyl diphosphate synthase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0003824 catalytic activity
GO:0009905 ent-copalyl diphosphate synthase activity
GO:0010333 terpene synthase activity
GO:0016829 lyase activity
GO:0016853 isomerase activity
GO:0046872 metal ion binding
Biological Process
GO:0008299 isoprenoid biosynthetic process
GO:0009686 gibberellin biosynthetic process
GO:0009740 gibberellic acid mediated signaling pathway
GO:0016102 diterpenoid biosynthetic process
Cellular Component
GO:0009507 chloroplast

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3pyb, PDBe:3pyb, PDBj:3pyb
PDBsum3pyb
PubMed
UniProtQ38802|KSA_ARATH Ent-copalyl diphosphate synthase, chloroplastic (Gene Name=GA1)

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