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Structure of PDB 3akz Chain A Binding Site BS02

Receptor Information

>3akz Chain A (length=463) Species: 243274 (Thermotoga maritima MSB8)

LVRVRFAPSPTGHLHVGGARTALFNWMFARKEGGKFILRIEDTDTERSSR
EYEQQILESLRWCGLDWDEGPDIGGDFGPYRQSERLEIYREYAEKLVEDK
RAYYVVYDKEDPSKELFTTYEYPHEYKEKGHPVTIKFKVLPGKTSFEDLL
KGYMEFDNSTLEDFIIMKSNGFPTYNFAVVVDDHLMRISHVFRGEDHLSN
TPKQLMIYEAFGWEAPVFMHIPLILGSDRTPLSKRHGATSVEHFRREGIL
SRALMNYLALLGWRVEGDEIFTIEEKLQSFDPKDISNKGVIFDYQKLEWV
NGKHMRRIDLEDLKREFIEWAKYAGKEIPSVDERYFSETLRICREKVNTL
SQLYDIMYPFMNDDYEYEKDYVEKFLKREEAERVLEEAKKAFKDLNSWNM
EEIEKTLRDLSEKGLASKKVVFQLIRGAVTGKLVTPGLFETIEVLGKERT
LKRLERTLQFLKK

Ligand information

• Ligand ID: GSU
• InChI: InChI=1S/C15H21N7O9S/c16-6(1-2-8(23)24)14(27)21-32(28,29)30-3-7-10(25)11(26)15(31-7)22-5-20-9-12(17)18-4-19-13(9)22/h4-7,10-11,15,25-26H,1-3,16H2,(H,21,27)(H,23,24)(H2,17,18,19)/t6-,7+,10+,11+,15+/m0/s1
• InChIKey: YBRKRYFZKHICLS-WERHYGNASA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COS(=O)(=O)NC(=O)C(CCC(=O)O)N)O)O)N
  CACTVS 3.341: N[C@@H](CCC(O)=O)C(=O)N[S](=O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COS(=O)(=O)NC(=O)[C@H](CCC(=O)O)N)O)O)N
  CACTVS 3.341: N[CH](CCC(O)=O)C(=O)N[S](=O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
  ACDLabs 10.04: O=C(O)CCC(N)C(=O)NS(=O)(=O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
• Formula: C15 H21 N7 O9 S
• Name: O5'-(L-GLUTAMYL-SULFAMOYL)-ADENOSINE
• ChEMBL: CHEMBL1163071
• ZINC: ZINC000014967046
• PDB chain: 3akz Chain A Residue 1001

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3akz Two enzymes bound to one transfer RNA assume alternative conformations for consecutive reactions.
• Resolution: 2.9 Å
• Binding residue (original residue number in PDB): R28 A30 P31 S32 H38 T44 E64 Y198 R216 G217 H220 L246 I247
• Binding residue (residue number reindexed from 1): R5 A7 P8 S9 H15 T21 E41 Y175 R193 G194 H197 L223 I224
• Annotation score: 2

Enzymatic activity

• Catalytic site (original residue number in PDB): S32 K257
• Catalytic site (residue number reindexed from 1): S9 K234
• Enzyme Commision number: 6.1.1.17: glutamate--tRNA ligase.

Gene Ontology

Molecular Function

• GO:0000049 tRNA binding
• GO:0000166 nucleotide binding
• GO:0004812 aminoacyl-tRNA ligase activity
• GO:0004818 glutamate-tRNA ligase activity
• GO:0005524 ATP binding
• GO:0008270 zinc ion binding

Biological Process

• GO:0006412 translation
• GO:0006418 tRNA aminoacylation for protein translation
• GO:0006424 glutamyl-tRNA aminoacylation
• GO:0043039 tRNA aminoacylation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol

External links

• PDB: RCSB:3akz, PDBe:3akz, PDBj:3akz
• PDBsum: 3akz
• PubMed: 20882017
• UniProt: Q9X2I8|SYE2_THEMA Glutamate--tRNA ligase 2 (Gene Name=gltX2)

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