Structure of PDB 3w3s Chain A Binding Site BS03

Receptor Information
>3w3s Chain A (length=527) Species: 190192 (Methanopyrus kandleri AV19) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MELKFSAEVELTLSREVDPAEIEPTVEEFVKEANEDLLQRGVPTGKEGAK
IESYYVLYDTIYMEITGTRYLRPHEAAMRVRKRLAERLGRKHRVGVRDLK
IPRYEVVLRFDREVTYDYVGYVPVADDVVVEDGTVRLTFQDVDEEMLRRH
VIDRVIRLVAWAVEERSELVERVTKVEPGTVVDESGPRRIRFRGDVTEEA
RRRGWVKEFPGRGQWIYTPPMAALFEVLRDFLLERVTRKLGFEPALFPKL
IPLETMFRMRYLHGLPDGMYYVCPPKRDPELFDDFKRELYVWGELNERTL
GSLKEKLRDPGYVLAPAQCEPFYELLRDEVVDPERLPIKLYDCSGWTYRW
EGGAAKGLERVNEFQRIEHVWIAEPEEAYRIRRELLEATKRVAEELELEW
KVVVSDDPFYLEGRLLEDRDIELPDVPSYEFEVYLPFKGERSSEEAWISV
GSFNVHGEHFVDGFNVKEKSGRTLFTGCAGLGVTRWVVGLLAQHGFYPYE
WPEPILERIDEKFGGLPEVPKTLTWPE
Ligand information
Ligand IDSSA
InChIInChI=1S/C13H19N7O8S/c14-5(1-21)12(24)19-29(25,26)27-2-6-8(22)9(23)13(28-6)20-4-18-7-10(15)16-3-17-11(7)20/h3-6,8-9,13,21-23H,1-2,14H2,(H,19,24)(H2,15,16,17)/t5-,6+,8+,9+,13+/m0/s1
InChIKeyHQXFJGONGJPTLZ-YTMOPEAISA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COS(=O)(=O)NC(=O)[C@H](CO)N)O)O)N
CACTVS 3.341N[CH](CO)C(=O)N[S](=O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
CACTVS 3.341N[C@@H](CO)C(=O)N[S](=O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
ACDLabs 10.04O=C(NS(=O)(=O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O)C(N)CO
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COS(=O)(=O)NC(=O)C(CO)N)O)O)N
FormulaC13 H19 N7 O8 S
Name5'-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE
ChEMBLCHEMBL1163070
DrugBankDB03869
ZINCZINC000013542770
PDB chain3w3s Chain A Residue 2002 [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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PDB3w3s Tertiary structure of bacterial selenocysteine tRNA
Resolution3.095 Å
Binding residue
(original residue number in PDB)		A317 R349 E351 V361 F364 R366 E368 F409 S449 V450 G451 S452 C478 G482 R485
Binding residue
(residue number reindexed from 1)		A317 R349 E351 V361 F364 R366 E368 F409 S449 V450 G451 S452 C478 G482 R485
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) C319 R349 E351 R360 E368 E430 S449 S452 C478 R485
Catalytic site (residue number reindexed from 1) C319 R349 E351 R360 E368 E430 S449 S452 C478 R485
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:0006418 tRNA aminoacylation for protein 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:3w3s, PDBe:3w3s, PDBj:3w3s
PDBsum3w3s
PubMed23649835
UniProtQ8TVD2|SYS2_METKA Type-2 serine--tRNA ligase (Gene Name=serS)

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