Structure of PDB 7mq9 Chain NK Binding Site BS01

Receptor Information

>7mq9 Chain NK (length=815) Species: 9606 (Homo sapiens)

MHRKKVDNRIRILIENGVAERQRSLFVVVGDRGKDQVVILHHMLSKATVK
ARPSVLWCYKKDPFELFIAATNIRYCYYNETHKILGNTFGMCVLQDFEAL
TPNLLARTVETVEGGGLVVILLRTMNSLKQLYTVTMDVHSRYRTEAHQDV
VGRFNERFILSLASCKKCLVIDDQLNILPISSHVATMEALPPSDLELREL
KESLQDTQPVGVLVDCCKTLDQAKAVLKFIEGISEKTLRSTVALTAARGR
GKSAALGLAIAGAVAFGYSNIFVTSPSPDNLHTLFEFVFKGFDALQYQEH
LDYEIIQSLNPEFNKAVIRVNVFREHRQTIQYIHPADAVKLGQAELVVID
EAAAIPLPLVKSLLGPYLVFMASTINGYEGTGRSLSLKLIQQLRQQARTL
YEVSLQESIRYAPGDAVEKWLNDLLCLDCLNITRIVSGCPLPEACELYYV
NRDTLFCYHKASEVFLQRLMALYVASHYKNSPNDLQMLSDAPAHHLFCLL
PPVPPTQNALPEVLAVIQVCLEGEISRQSILNSLSRGDLIPWTVSEQFQD
PDFGGLSGGRVVRIAVHPDYQGMGYGSRALQLLQMYYEGRFPEEVITPRK
DLPPLLLKLNERPAERLDYLGVSYGLTPRLLKFWKRAGFVPVYLRQTPND
LTGEHSCIMLKTLGWLAAFWKDFRRRFLALLSYQFSTFSPSLALNIIQNR
NMGKPAQPALSREELEALFLPYDLKRLEMYSRNMVDYHLIMDMIPAISRI
YFLNQLGDLALSAAQSALLLGIGLQHKSVDQLEKEIELPSGQLMGLFNRI
IRKVVKLFNEVQEKA

Ligand information

• Ligand ID: ATP
• InChI: InChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
• InChIKey: ZKHQWZAMYRWXGA-KQYNXXCUSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=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[P](O)(O)=O)[CH](O)[CH]3O
  ACDLabs 10.04: O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
  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)OP(=O)(O)O)O)O)N
  CACTVS 3.341: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
• Formula: C10 H16 N5 O13 P3
• Name: ADENOSINE-5'-TRIPHOSPHATE
• ChEMBL: CHEMBL14249
• DrugBank: DB00171
• ZINC: ZINC000004261765
• PDB chain: 7mq9 Chain NK Residue 1101

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7mq9 Nucleolar maturation of the human small subunit processome.
• Resolution: 3.87 Å
• Binding residue (original residue number in PDB): K256 G287 G289 K290 S291
• Binding residue (residue number reindexed from 1): K218 G249 G251 K252 S253
• Annotation score: 5

Enzymatic activity

• Enzyme Commision number: 2.3.1.-

Gene Ontology

Molecular Function

• GO:0000049 tRNA binding
• GO:0003723 RNA binding
• GO:0005515 protein binding
• GO:0005524 ATP binding
• GO:0008080 N-acetyltransferase activity
• GO:0016746 acyltransferase activity
• GO:0016747 acyltransferase activity, transferring groups other than amino-acyl groups
• GO:0051392 tRNA N-acetyltransferase activity
• GO:0070182 DNA polymerase binding
• GO:0106162 mRNA N-acetyltransferase activity
• GO:1990883 rRNA cytidine N-acetyltransferase activity

Biological Process

• GO:0000154 rRNA modification
• GO:0006364 rRNA processing
• GO:0006417 regulation of translation
• GO:0006473 protein acetylation
• GO:0008033 tRNA processing
• GO:0010824 regulation of centrosome duplication
• GO:0016072 rRNA metabolic process
• GO:0032211 negative regulation of telomere maintenance via telomerase
• GO:0042274 ribosomal small subunit biogenesis
• GO:0045727 positive regulation of translation
• GO:0051391 tRNA acetylation
• GO:1904812 rRNA acetylation involved in maturation of SSU-rRNA

Cellular Component

• GO:0000781 chromosome, telomeric region
• GO:0005634 nucleus
• GO:0005654 nucleoplasm
• GO:0005697 telomerase holoenzyme complex
• GO:0005730 nucleolus
• GO:0016020 membrane
• GO:0030496 midbody
• GO:0032040 small-subunit processome

External links

• PDB: RCSB:7mq9, PDBe:7mq9, PDBj:7mq9
• PDBsum: 7mq9
• PubMed: 34516797
• UniProt: Q9H0A0|NAT10_HUMAN RNA cytidine acetyltransferase (Gene Name=NAT10)