Structure of PDB 6ec8 Chain A Binding Site BS01

Receptor Information

>6ec8 Chain A (length=803) Species: 469371 (Thermobispora bispora DSM 43833)

PKVAVRECGLPVSAIESLCCTDSFALIRRQVRETAWLKGEGKRLAVDLGL
LIGERGPVLVGLRRALHTGRLPDAREWTPRVASALPAELAARVADWVTRM
RALTRARRELPELFAAEARVKEKVLAQVAADPGFRRALSLASPELAADLD
RWLAEPARRPKTQKLLRLAKYVARAAVKTSPYSTFTSMGVAVWENGEDWA
DGAIVRFAPREPPSVILEPSGEWLHGALRAWLARPENLVRSRLRLNPSLV
IRADKAEFLGFPPREPIIRMGLTPVVATVLRLAEPAADADGWIDPMGFRD
RLARDLPAEPEQVDRLLRSLIEAGVLEAHPLTRAGLPETGEWAEIRAALR
HDPHGEDPEAYRVRLARLKRAMTMMWPQGDTTALLHETAVVTRPVASLNP
TAWGRGLSDLDVVRRWLSVFDGKLPIRIVVAEYLRARYGEHARVPFLTFH
RHVQEEIAGDAPSGADLRTFVGRSAAIWAPPLAHSRLPRLRELAKLREAA
RELALGRPEHDGIQRVDPEELIKQMATWPEWIVVPRSCACYVQPAPEGRL
VLNVVHGGHGRGLRRLSHLIGRVRGEAVDHPMVADEPEGTVYAELSGSLG
STLNVHVPGTRYEIDYPFSPGDRSRDRRLPLSDLEVVLAPETGLAELRSR
RLGFRVIPLHLGMAAEFQLPPAARFLERAFGVTYLPQEVTRYPRVEVGRV
VVQRRRWLAPAGTLPIRAKGEDDASYLLRLVAWTDANGIPTRSFVRKPLF
LDLANPFLVKVFERQIRDCAFVLFEEALPDPADAPPREGSDLPRVIEFLV
ELG

Ligand information

• Ligand ID: J4G
• InChI: InChI=1S/C15H22N7O9P/c16-6(1-2-8(23)24)14(26)21-9-7(3-30-32(27,28)29)31-15(11(9)25)22-5-20-10-12(17)18-4-19-13(10)22/h4-7,9,11,15,25H,1-3,16H2,(H,21,26)(H,23,24)(H2,17,18,19)(H2,27,28,29)/t6-,7+,9+,11+,15+/m0/s1
• InChIKey: SDRBGGWQNQDMBH-HQMNMZSFSA-N
• SMILES:
  ACDLabs 12.01: NC(C(NC3C(C(n2c1c(c(ncn1)N)nc2)OC3COP(O)(=O)O)O)=O)CCC(O)=O
  CACTVS 3.385: N[C@@H](CCC(O)=O)C(=O)N[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(O)=O)n2cnc3c(N)ncnc23
  OpenEye OEToolkits 2.0.6: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)O)NC(=O)C(CCC(=O)O)N)O)N
  CACTVS 3.385: N[CH](CCC(O)=O)C(=O)N[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=O)n2cnc3c(N)ncnc23
  OpenEye OEToolkits 2.0.6: c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)NC(=O)[C@H](CCC(=O)O)N)O)N
• Formula: C15 H22 N7 O9 P
• Name: 3'-deoxy-3'-[(L-alpha-glutamyl)amino]adenosine 5'-(dihydrogen phosphate)
• PDB chain: 6ec8 Chain A Residue 901

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6ec8 Characterization of glutamyl-tRNA-dependent dehydratases using nonreactive substrate mimics.
• Resolution: 2.148 Å
• Binding residue (original residue number in PDB): R197 K201 T202 S203 Y564 R743 F783 E829 L832 E851
• Binding residue (residue number reindexed from 1): R174 K178 T179 S180 Y541 R704 F744 E775 L778 E797
• Annotation score: 1

External links

• PDB: RCSB:6ec8, PDBe:6ec8, PDBj:6ec8
• PDBsum: 6ec8
• PubMed: 31409709
• UniProt: D6Y502