Structure of PDB 2vwb Chain B Binding Site BS01

Receptor Information
>2vwb Chain B (length=507) Species: 243232 (Methanocaldococcus jannaschii DSM 2661) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MICLGLEGTAEKTGVGIVTSDGEVLFNKTIMEAADHHAETFPKLIKEAFE
VVDKNEIDLIAFSQGPGLGPSLRVTATVARTLSLTLKKPIIGVNHCIAHI
EIGKLTTEAEDPLTLYVSGGNTQVIAYVSKKYRVFGETLDIAVGNCLDQF
ARYVNLPHPGGPYIEELARKGKKLVDLPYTVKGMDIAFSGLLTAAMRAYD
AGERLEDICYSLQEYAFSMLTEITERALAHTNKGEVMLVGGVAANNRLRE
MLKAMCEGQNVDFYVPPKEFCGDNGAMIAWLGLLMHKNGRWMSLDETKII
PNYRTDMVEVNWIKGKGAEADIKRDSYLDFDVIIKERVKKGYRDERLDEN
IRKSRTAREARYLALVKDFGIPAPYIFDVDLDNKRIMMSYINGKLAKDVI
EDNLDIAYKIGEIVGKLHKNDVIHNDLTTSNFIFDKDLYIIDFGLGKISN
LDEDKAVDLIVFKKAVLSTHHEKFDEIWERFLEGYKSVYDRWEIILELMK
DVERRAR
Ligand information
Ligand IDANP
InChIInChI=1S/C10H17N6O12P3/c11-8-5-9(13-2-12-8)16(3-14-5)10-7(18)6(17)4(27-10)1-26-31(24,25)28-30(22,23)15-29(19,20)21/h2-4,6-7,10,17-18H,1H2,(H,24,25)(H2,11,12,13)(H4,15,19,20,21,22,23)/t4-,6-,7-,10-/m1/s1
InChIKeyPVKSNHVPLWYQGJ-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N
CACTVS 3.370Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)[CH](O)[CH]3O
CACTVS 3.370Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)[C@@H](O)[C@H]3O
ACDLabs 12.01O=P(O)(O)NP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(NP(=O)(O)O)O)O)O)N
FormulaC10 H17 N6 O12 P3
NamePHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
ChEMBLCHEMBL1230989
DrugBank
ZINCZINC000008660410
PDB chain2vwb Chain B Residue 1533 [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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PDB2vwb Structure of the Archaeal Kae1/Bud32 Fusion Protein Mj1130: A Model for the Eukaryotic Ekc/Keops Subcomplex
Resolution3.05 Å
Binding residue
(original residue number in PDB)		A10 K12 H106 H110 Y127 S129 G130 G131 G155 L158 D159 P170 G172 P173 G252 A255 N256 D284
Binding residue
(residue number reindexed from 1)		A10 K12 H95 H99 Y116 S118 G119 G120 G144 L147 D148 P159 G161 P162 G241 A244 N245 D273
Annotation score3
Enzymatic activity
Enzyme Commision number 2.3.1.234: N(6)-L-threonylcarbamoyladenine synthase.
2.7.11.1: non-specific serine/threonine protein kinase.
Gene Ontology
Molecular Function
GO:0004222 metalloendopeptidase activity
GO:0004672 protein kinase activity
GO:0004674 protein serine/threonine kinase activity
GO:0004712 protein serine/threonine/tyrosine kinase activity
GO:0005506 iron ion binding
GO:0005524 ATP binding
GO:0008270 zinc ion binding
GO:0016746 acyltransferase activity
GO:0016747 acyltransferase activity, transferring groups other than amino-acyl groups
GO:0044024 histone H2AS1 kinase activity
GO:0046872 metal ion binding
GO:0061711 N(6)-L-threonylcarbamoyladenine synthase activity
GO:0106310 protein serine kinase activity
Biological Process
GO:0002949 tRNA threonylcarbamoyladenosine modification
GO:0006338 chromatin remodeling
GO:0006400 tRNA modification
GO:0006468 protein phosphorylation
GO:0008033 tRNA processing
GO:0016310 phosphorylation
GO:0070525 tRNA threonylcarbamoyladenosine metabolic process
Cellular Component
GO:0000408 EKC/KEOPS complex
GO:0005737 cytoplasm

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:2vwb, PDBe:2vwb, PDBj:2vwb
PDBsum2vwb
PubMed19172740
UniProtQ58530|KAE1B_METJA Probable bifunctional tRNA threonylcarbamoyladenosine biosynthesis protein (Gene Name=MJ1130)

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