Structure of PDB 5o5z Chain A Binding Site BS01

Receptor Information

>5o5z Chain A (length=454) Species: 2265 (Thermococcus litoralis)

MKESLKDRIRLWKRLYVNAFENALNAIPNVKGVLLAYNTNIDAIKYLDAD
DLEKRVTEKGKEKVFEIIENPPEKISSIEELLGGILRSIKLGKAMEWFVE
SEEVRRYLREWGWDELRIGGQAGIMANLLGGVYRIPTIVHVPQNPKLQAE
LFVDGPIYVPVFEGNKLKLVHPKDAIAEEEELIHYIYEFPRGFQVFDVQA
PRENRFIANADDYNARVYMRREFREGFEEITRNVELAIISGLQVLKEYYP
DGTTYKDVLDRVESHLNILNRYNVKSHFEFAYTANRRVREALVELLPKFT
SVGLNEVELASIMEIIGDEELAKEVLEGHIFSVIDAMNVLMDETGIERIH
FHTYGYYLALTQGGGRQLAFVPTKIVASPKSTVGIGDTISSSAFVSEFGG
GGGVRDALLFASLAAAAKAMKGNLERIEQIRDALSVPTNERAIVLEEELE
KEFT

Ligand information

• Ligand ID: AT4
• InChI: InChI=1S/C10H15N5O9P2S/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(23-10)1-22-25(18,19)24-26(20,21)27/h2-4,6-7,10,16-17H,1H2,(H,18,19)(H2,11,12,13)(H2,20,21,27)/t4-,6-,7-,10-/m1/s1
• InChIKey: HCIKUKNAJRJFOW-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)O[P@@](=O)(O)S)O)O)N
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)S)O)O)N
  CACTVS 3.341: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@@](O)(S)=O)[C@@H](O)[C@H]3O
  ACDLabs 10.04: O=P(O)(S)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
  CACTVS 3.341: Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(S)=O)[CH](O)[CH]3O
• Formula: C10 H15 N5 O9 P2 S
• Name: 5'-O-[(R)-HYDROXY(THIOPHOSPHONOOXY)PHOSPHORYL]ADENOSINE;
  ADENOSINE 5'-O-(2-THIODIPHOSPHATE)
• ChEMBL: CHEMBL335206
• PDB chain: 5o5z Chain A Residue 508

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5o5z Protein topology determines substrate-binding mechanism in homologous enzymes.
• Resolution: 2.441 Å
• Binding residue (original residue number in PDB): N305 H352 T353 V376 I385 G386 I389
• Binding residue (residue number reindexed from 1): N305 H352 T353 V376 I385 G386 I389
• Annotation score: 4

Enzymatic activity

• Enzyme Commision number: 2.7.1.-
  2.7.1.147: ADP-specific glucose/glucosamine kinase.

Gene Ontology

Molecular Function

• GO:0016773 phosphotransferase activity, alcohol group as acceptor

Biological Process

• GO:0005975 carbohydrate metabolic process

External links

• PDB: RCSB:5o5z, PDBe:5o5z, PDBj:5o5z
• PDBsum: 5o5z
• PubMed: 30251675
• UniProt: Q7M537|GLKA_THELN ADP-dependent glucose/glucosamine kinase (Gene Name=glkA)