Structure of PDB 5j99 Chain A Binding Site BS01

Receptor Information

>5j99 Chain A (length=356) Species: 6850 (Limulus polyphemus)

VDQATLDKLEAGFKKLQEASDCKSLLKKHLTKDVFDSIKNKKTGMGATLL
DVIQSGVENLDSGVGIYAPDAESYRTFGPLFDPIIDDYHGGFKLTDKHPP
KQWGDINTLVGLDPAGQFIISTRVRCGRSLQGYPFNPCLTAEQYKEMEEK
VSSTLSSMEDELKGTYYPLTGMSKATQQQLIDDHFLFKEGDRFLQTANAC
RYWPTGRGIFHNDAKTFLVWVNEEDHLRIISMQKGGDLKTVYKRLVTAVD
NIESKLPFSHDDRFGFLTFCPTNLGTTMRASVHIQLPKLAKDRKVLEDIA
SKFNLQVRGTRGEHTESEGGVYDISNKRRLGLTEYQAVREMQDGILEMIK
MEKAAA

Ligand information

• Ligand ID: ADP
• InChI: InChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
• InChIKey: XTWYTFMLZFPYCI-KQYNXXCUSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N
  CACTVS 3.341: Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
  ACDLabs 10.04: O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
  CACTVS 3.341: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
• Formula: C10 H15 N5 O10 P2
• Name: ADENOSINE-5'-DIPHOSPHATE
• ChEMBL: CHEMBL14830
• DrugBank: DB16833
• ZINC: ZINC000012360703
• PDB chain: 5j99 Chain A Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5j99 The Sampling of Conformational Dynamics in Ambient-Temperature Crystal Structures of Arginine Kinase.
• Resolution: 1.7 Å
• Binding residue (original residue number in PDB): S122 R124 R126 H185 R229 R280 S282 V283 H284 R309 R312 G313 D324
• Binding residue (residue number reindexed from 1): S121 R123 R125 H184 R228 R279 S281 V282 H283 R308 R311 G312 D323
• Annotation score: 5

Enzymatic activity

• Catalytic site (original residue number in PDB): R126 E225 R229 C271 T273 R280 R309 E314
• Catalytic site (residue number reindexed from 1): R125 E224 R228 C270 T272 R279 R308 E313
• Enzyme Commision number: 2.7.3.3: arginine kinase.

Gene Ontology

Molecular Function

• GO:0003824 catalytic activity
• GO:0004054 arginine kinase activity
• GO:0004111 creatine kinase activity
• GO:0005524 ATP binding
• GO:0016301 kinase activity
• GO:0016772 transferase activity, transferring phosphorus-containing groups

Biological Process

• GO:0016310 phosphorylation
• GO:0046314 phosphocreatine biosynthetic process

Cellular Component

• GO:0005737 cytoplasm

External links

• PDB: RCSB:5j99, PDBe:5j99, PDBj:5j99
• PDBsum: 5j99
• PubMed: 27594681
• UniProt: P51541|KARG_LIMPO Arginine kinase