Structure of PDB 4rrc Chain A Binding Site BS01

Receptor Information

>4rrc Chain A (length=136) Species: 272557 (Aeropyrum pernix K1)

MRLLYLHADRFEYKTVKPALKNPPDPPGEASFGEALVVFTTVEDGDGPQT
VMYAASDIASHSSRLKVTTVILYPYAHLSSRLAKPMAAHKRLIELEGALR
TKFPGHVHRAPFGWYKSFSIACKGHPLAELSRSFTE

Ligand information

• Ligand ID: A3T
• InChI: InChI=1S/C14H21N7O5/c1-5(23)7(15)13(25)20-8-6(2-22)26-14(10(8)24)21-4-19-9-11(16)17-3-18-12(9)21/h3-8,10,14,22-24H,2,15H2,1H3,(H,20,25)(H2,16,17,18)/t5-,6-,7+,8-,10-,14-/m1/s1
• InChIKey: JYCQZCJEBNTMCV-JHJLZTHQSA-N
• SMILES:
  OpenEye OEToolkits 1.7.0: CC(C(C(=O)NC1C(OC(C1O)n2cnc3c2ncnc3N)CO)N)O
  OpenEye OEToolkits 1.7.0: C[C@H]([C@@H](C(=O)N[C@@H]1[C@H](O[C@H]([C@@H]1O)n2cnc3c2ncnc3N)CO)N)O
  CACTVS 3.370: C[CH](O)[CH](N)C(=O)N[CH]1[CH](O)[CH](O[CH]1CO)n2cnc3c(N)ncnc23
  CACTVS 3.370: C[C@@H](O)[C@H](N)C(=O)N[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO)n2cnc3c(N)ncnc23
  ACDLabs 12.01: O=C(NC3C(OC(n2cnc1c(ncnc12)N)C3O)CO)C(N)C(O)C
• Formula: C14 H21 N7 O5
• Name: 3'-deoxy-3'-(L-threonylamino)adenosine
• ZINC: ZINC000058631685
• PDB chain: 4rrc Chain A Residue 500

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4rrc Specificity and catalysis hardwired at the RNA-protein interface in a translational proofreading enzyme.
• Resolution: 1.86 Å
• Binding residue (original residue number in PDB): V42 Y75 A76 A88 F112 G113 W114 Y115
• Binding residue (residue number reindexed from 1): V42 Y75 A76 A88 F112 G113 W114 Y115
• Annotation score: 2
• Binding affinity: MOAD: Kd=13.4uM

Enzymatic activity

• Enzyme Commision number: 6.1.1.3: threonine--tRNA ligase.

Gene Ontology

Molecular Function

• GO:0004829 threonine-tRNA ligase activity
• GO:0005524 ATP binding
• GO:0008270 zinc ion binding

Cellular Component

• GO:0005737 cytoplasm

External links

• PDB: RCSB:4rrc, PDBe:4rrc, PDBj:4rrc
• PDBsum: 4rrc
• PubMed: 26113036
• UniProt: Q9YFY3|SYTE_AERPE Threonine--tRNA ligase editing subunit (Gene Name=thrS2)