Structure of PDB 8qrn Chain 7 Binding Site BS04

Receptor Information
>8qrn Chain 7 (length=571) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DKVRKNKDAVRRPQADPALLTPRSPVVTIMGHVDHGKTTLLDKFRKTQVA
AVETGGITQHIGAFLVSLPSGEKITFLDTPGHAAFSAMRARGAQVTDIVV
LVVAADDGVMKQTVESIQHAKDAQVPIILAVNKCDKAEADPEKVKKELLA
YDVVCEDYGGDVQAVPVSALTGDNLMALAEATVALAEMLELKADPNGPVE
GTVIESFTDKGRGLVTTAIIQRGTLRKGSVLVAGKCWAKVRLMFDENGKT
IDEAYPSMPVGITGWRDLPSAGEEILEVESEPRAREVVDWRKYEQEQEKG
QEDLKIIEEKRKEHKEAHQKAREKYGHLLWKKRSILRFLERKEQIPLKPK
EKRERDSNVLSVIIKGDVDGSVEAILNIIDTYDASHECELELVHFGVGDV
SANDVNLAETFDGVIYGFNVNAGNVIQQSAAKKGVKIKLHKIIYRLVEDL
QEELSSRLPCAVEEHPVGEASILATFSVTEGKKKVPVAGCRVQKGQLEKQ
KKFKLTRNGHVIWKGSLTSLKHHKDDISIVKTGMDCGLSLDEDNMEFQVG
DRIVCYEEKQIQAKTSWDPGF
Ligand information
Ligand IDGTP
InChIInChI=1S/C10H16N5O14P3/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(27-9)1-26-31(22,23)29-32(24,25)28-30(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H,24,25)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
InChIKeyXKMLYUALXHKNFT-UUOKFMHZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1nc2c(n1[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=C(NC2=O)N
CACTVS 3.370NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
CACTVS 3.370NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
OpenEye OEToolkits 1.7.6c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
FormulaC10 H16 N5 O14 P3
NameGUANOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL1233147
DrugBankDB04137
ZINCZINC000060094177
PDB chain8qrn Chain 7 Residue 801 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB8qrn GTPBP8 plays a role in mitoribosome formation in human mitochondria.
Resolution2.98 Å
Binding residue
(original residue number in PDB)		D190 H191 G192 K193 T194 T195 I213 T214 G237 N288 K289 D291 L326
Binding residue
(residue number reindexed from 1)		D34 H35 G36 K37 T38 T39 I57 T58 G81 N132 K133 D135 L170
Annotation score4
Gene Ontology
Molecular Function
GO:0003723 RNA binding
GO:0003743 translation initiation factor activity
GO:0005525 GTP binding
GO:0008135 translation factor activity, RNA binding
GO:0043024 ribosomal small subunit binding
Biological Process
GO:0006412 translation
GO:0006413 translational initiation
GO:0006446 regulation of translational initiation
GO:0032790 ribosome disassembly
GO:0070124 mitochondrial translational initiation
Cellular Component
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005739 mitochondrion

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:8qrn, PDBe:8qrn, PDBj:8qrn
PDBsum8qrn
PubMed38969660
UniProtP46199|IF2M_HUMAN Translation initiation factor IF-2, mitochondrial (Gene Name=MTIF2)

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