Structure of PDB 5ksd Chain B Binding Site BS01

Receptor Information
>5ksd Chain B (length=833) Species: 3702 (Arabidopsis thaliana) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VDLEKIPIEEVFQQLKCSREGLTTQEGEDRIQIFGPNKLEEKKESKLLKF
LGFMWNPLSWVMEMAAIMAIALANGDGRPPDWQDFVGIICLLVINSTISF
IEENNAGNAAAALMAGLAPKTKVLRDGKWSEQEAAILVPGDIVSIKLGDI
IPADARLLEGDPLKVDQSALTGESLPVTKHPGQEVFSGSTCKQGEIEAVV
IATGVHTFFGKAAHLVDSTNQVGHFQKVLTAIGNFCICSIAIGMVIEIIV
MYPIQRRKYRDGIDNLLVLLIGGIPIAMPTVLSVTMAIGSHRLSQQGAIT
KRMTAIEEMAGMDVLCSDKTGTLTLNKLSVDKNLVEVFCKGVEKDQVLLF
AAMASRVENQDAIDAAMVGMLADPKEARAGIREVHFLPFNPVDKRTALTY
IDGSGNWHRVSKGAPEQILELAKASNDLSKKVLSIIDKYAERGLRSLAVA
RQVVPEKTKESPGAPWEFVGLLPLFDPPRHDSAETIRRALNLGVNVKMIT
GDQLAIGKETGRRLGMGTNMYPSSALLGTHKDANLASIPVEELIEKADGF
AGVFPEHKYEIVKKLQERKHIVGMTGDGVNDAPALKKADIGIAVADATDA
ARGASDIVLTEPGLSVIISAVLTSRAIFQRMKNYTIYAVSITIRIVFGFM
LIALIWEFDFSAFMVLIIAILNDGTIMTISKDRVKPSPTPDSWKLKEIFA
TGVVLGGYQAIMTVIFFWAAHKTDFFSDTFGVRSIRDNNHELMGAVYLQV
SIISQALIFVTRSRSWSFVERPGALLMIAFLIAQLIATLIAVYANWEFAK
IRGIGWGWAGVIWLYSIVTYFPLDVFKFAIRYI
Ligand information
Ligand IDACP
InChIInChI=1S/C11H18N5O12P3/c12-9-6-10(14-2-13-9)16(3-15-6)11-8(18)7(17)5(27-11)1-26-31(24,25)28-30(22,23)4-29(19,20)21/h2-3,5,7-8,11,17-18H,1,4H2,(H,22,23)(H,24,25)(H2,12,13,14)(H2,19,20,21)/t5-,7-,8-,11-/m1/s1
InChIKeyUFZTZBNSLXELAL-IOSLPCCCSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)C[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)CP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(CP(=O)(O)O)O)O)O)N
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@](=O)(CP(=O)(O)O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@](O)(=O)C[P](O)(O)=O)[C@@H](O)[C@H]3O
FormulaC11 H18 N5 O12 P3
NamePHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER;
ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE
ChEMBLCHEMBL133463
DrugBankDB03909
ZINCZINC000008295124
PDB chain5ksd Chain B Residue 904 [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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PDB5ksd Improved Model of Proton Pump Crystal Structure Obtained by Interactive Molecular Dynamics Flexible Fitting Expands the Mechanistic Model for Proton Translocation in P-Type ATPases.
Resolution3.5 Å
Binding residue
(original residue number in PDB)		T331 I374 F400 A425 L458 T511
Binding residue
(residue number reindexed from 1)		T320 I363 F389 A414 L447 T500
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) D329 D588 D592
Catalytic site (residue number reindexed from 1) D318 D577 D581
Enzyme Commision number 7.1.2.1: P-type H(+)-exporting transporter.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0005215 transporter activity
GO:0005524 ATP binding
GO:0008553 P-type proton-exporting transporter activity
GO:0016887 ATP hydrolysis activity
Biological Process
GO:0120029 proton export across plasma membrane
Cellular Component
GO:0016020 membrane

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5ksd, PDBe:5ksd, PDBj:5ksd
PDBsum5ksd
PubMed28443028
UniProtP19456|PMA2_ARATH ATPase 2, plasma membrane-type (Gene Name=AHA2)

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