Structure of PDB 2cja Chain B Binding Site BS04

Receptor Information
>2cja Chain B (length=489) Species: 269797 (Methanosarcina barkeri str. Fusaro) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GSHMKLQFNLKAYFKTSADPTPAKDAIAALFEEANSTLLTRGAPEGQGAK
VTEWKLGEDRIELTLQSGRYVRVHDAIFRLRKQLAEALGKKYKIGIRGIE
VESFIIKVPADHELRMLKVPYIKSMENIEGGIQLELEVGEAEMKNRVPDR
ILTLLEEKIEAAQYGAKAEHWNLLWQREPMEHPFKEDPTQAMMKEGWLKR
GSSRGQWIHGPQSARIFRTFEKIVLEELLEPLGYREMIFPKLVTWEVWMK
SGHAKGVYPEIYYVCPPQTRDPDYWEEVADYYKVTHEVPTKLIKEKIAEP
IGGMCYAQCPPFWMYVAGETLPNEEIPVKVFDRSGTSHRYESGGIHGIER
VDEFHRIEIVWIGTKEEVLKCAEELHDRYMHIFNDILDIEWRKARVNTVG
TTDYEACLPYRGPDGEWLEFQNVSINGDKYPKGFNVKLQSGDELWSGCSG
VGLERWAAVFLAQKGLDPANWPEEFRNRVGEMPKGIRFL
Ligand information
Ligand IDATP
InChIInChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyZKHQWZAMYRWXGA-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
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)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
FormulaC10 H16 N5 O13 P3
NameADENOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL14249
DrugBankDB00171
ZINCZINC000004261765
PDB chain2cja Chain B Residue 1507 [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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PDB2cja Structure of the Unusual Seryl-tRNA Synthetase Reveals a Distinct Zinc-Dependent Mode of Substrate Recognition
Resolution2.2 Å
Binding residue
(original residue number in PDB)		R336 E338 R347 V348 F351 R353 E432 G465 R468
Binding residue
(residue number reindexed from 1)		R339 E341 R350 V351 F354 R356 E419 G452 R455
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) C306 R336 E338 R347 E355 D416 E432 N435 C461 R468
Catalytic site (residue number reindexed from 1) C309 R339 E341 R350 E358 D403 E419 N422 C448 R455
Enzyme Commision number 6.1.1.11: serine--tRNA ligase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0004812 aminoacyl-tRNA ligase activity
GO:0004828 serine-tRNA ligase activity
GO:0005524 ATP binding
GO:0008270 zinc ion binding
GO:0046872 metal ion binding
Biological Process
GO:0006412 translation
GO:0006434 seryl-tRNA aminoacylation
GO:0016260 selenocysteine biosynthetic process
Cellular Component
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:2cja, PDBe:2cja, PDBj:2cja
PDBsum2cja
PubMed16675947
UniProtQ46AN5|SYS2_METBF Type-2 serine--tRNA ligase (Gene Name=serS2)

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