Structure of PDB 6c86 Chain B Binding Site BS01

Receptor Information

>6c86 Chain B (length=497) Species: 353152 (Cryptosporidium parvum Iowa II)

SHYTDNRYKMMECIKDAGRPFYPHKFKISMSLPAYALKYGNVENGYIDKD
TTLSLSGRVTSIRSSSSKLIFYDIFCEEQKVQIIANIMEHDISTGEFSVS
HSEIRRGDVVGFTGFPGKSKRGELSLFSKSVVLLSPCYHMLPTAIDQEVR
YRQRYLDLMLNEESRKVFKLRSRAIKYIRNYFDRLGFLEVETPMLNMIYG
GAAARPFITYHNELETQLYMRIAPELYLKQLIVGGLDKVYEIGKNFRNEG
IDLTHNPEFTAMEFYMAYADYYDLMDLTEELISGLVLEIHGSLKIPYHPD
GPEGKCIEIDFTTPWKRFSFVEEIESGLGEKLKRPLDSQENIDFMVEMCE
KHEIELPHPRTAAKLLDKLAGHFVETKCTNPSFIIDHPQTMSPLAKWHRE
KPEMTERFELFVLGKELCNAYTELNEPLQQRKFFEQQADAKASGDVEACP
IDETFCLALEHGLPPTGGWGLGIDRLIMFLADKNNIKEVILFPAMRN

Ligand information

• Ligand ID: KAA
• InChI: InChI=1S/C16H26N8O7S/c17-4-2-1-3-8(18)15(27)23-32(28,29)30-5-9-11(25)12(26)16(31-9)24-7-22-10-13(19)20-6-21-14(10)24/h6-9,11-12,16,25-26H,1-5,17-18H2,(H,23,27)(H2,19,20,21)/t8-,9+,11+,12+,16+/m0/s1
• InChIKey: NARKTLKJPPMFJF-LEJQEAHTSA-N
• SMILES:
  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](CCCCN)N)O)O)N
  CACTVS 3.341: NCCCC[CH](N)C(=O)N[S](=O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
  CACTVS 3.341: NCCCC[C@H](N)C(=O)N[S](=O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
  ACDLabs 10.04: O=C(NS(=O)(=O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O)C(N)CCCCN
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COS(=O)(=O)NC(=O)C(CCCCN)N)O)O)N
• Formula: C16 H26 N8 O7 S
• Name: 5'-O-[(L-LYSYLAMINO)SULFONYL]ADENOSINE;
  5'-O-[N-(L-LYSYL)SULFAMOYL]ADENOSINE
• ChEMBL: CHEMBL1163083
• ZINC: ZINC000040956727
• PDB chain: 6c86 Chain B Residue 601

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6c86 Crystal Structure of Lysyl-tRNA Synthetase from Cryptosporidium parvum complexed with L-Lysylsulfamoyl Adenosine
• Resolution: 2.15 Å
• Binding residue (original residue number in PDB): G249 A271 E273 R295 T302 H303 N304 F307 E311 Y313 E464 L465 N467 Y469 E471 G516 W517 G518 G520 R523
• Binding residue (residue number reindexed from 1): G201 A223 E225 R247 T254 H255 N256 F259 E263 Y265 E416 L417 N419 Y421 E423 G468 W469 G470 G472 R475
• Annotation score: 2

Enzymatic activity

• Catalytic site (original residue number in PDB): R295 E297 T302 H303 E464 N467 R523
• Catalytic site (residue number reindexed from 1): R247 E249 T254 H255 E416 N419 R475
• Enzyme Commision number: 6.1.1.6: lysine--tRNA ligase.

Gene Ontology

Molecular Function

• GO:0000049 tRNA binding
• GO:0000166 nucleotide binding
• GO:0003676 nucleic acid binding
• GO:0004812 aminoacyl-tRNA ligase activity
• GO:0004824 lysine-tRNA ligase activity
• GO:0005524 ATP binding

Biological Process

• GO:0006418 tRNA aminoacylation for protein translation
• GO:0006430 lysyl-tRNA aminoacylation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0016020 membrane

External links

• PDB: RCSB:6c86, PDBe:6c86, PDBj:6c86
• PDBsum: 6c86
• UniProt: Q5CR27