Structure of PDB 7nfx Chain x Binding Site BS02

Receptor Information
>7nfx Chain x (length=417) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LADLGRKITSALRSLSNATIINEEVLNAMLKEVCTALLEADVNIKLVKQL
RENVKSAIDLEEMASGLNKRKMIQHAVFKELVKLVDPGVKAWTPTKGKQN
VIMFVGLQGSGKTTTCSKLAYYYQRKGWKTCLICADTFRAGAFDQLKQNA
TKARIPFYGSYTEMDPVIIASEGVEKFKNENFEIIIVDTSGRHKQEDSLF
EEMLQVANAIQPDNIVYVMDASIEQACEAQAKAFKDKVDVASVIVTKLDG
HAKGGGALSAVAATKSPIIFIGTGEHIDDFEPFKTQPFISKLLGMGDIEG
LIDKVNELKLDDNEALIEKLKHGQFTLRDMYEQFQNIMKMGPGNEQESMA
RLKKLMTIMDSMNDQELDSTDGAKVFSKQPGRIQRVARGSGVSTRDVQEL
LTQYTKFAQMVKKMGGI
Ligand information
Ligand IDGNP
InChIInChI=1S/C10H17N6O13P3/c11-10-13-7-4(8(19)14-10)12-2-16(7)9-6(18)5(17)3(28-9)1-27-32(25,26)29-31(23,24)15-30(20,21)22/h2-3,5-6,9,17-18H,1H2,(H,25,26)(H3,11,13,14,19)(H4,15,20,21,22,23,24)/t3-,5-,6-,9-/m1/s1
InChIKeyUQABYHGXWYXDTK-UUOKFMHZSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=P(O)(O)NP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(NP(=O)(O)O)O)O)O)N=C(NC2=O)N
OpenEye OEToolkits 1.5.0c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N=C(NC2=O)N
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P@@](O)(=O)N[P](O)(O)=O)[C@@H](O)[C@H]3O
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)[CH](O)[CH]3O
FormulaC10 H17 N6 O13 P3
NamePHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
ChEMBLCHEMBL1233085
DrugBankDB02082
ZINCZINC000037868676
PDB chain7nfx Chain x Residue 601 [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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PDB7nfx Receptor compaction and GTPase rearrangement drive SRP-mediated cotranslational protein translocation into the ER.
Resolution3.2 Å
Binding residue
(original residue number in PDB)		G111 S112 G113 K114 T115 T116 R141 K249 G274 T275 G276 E277
Binding residue
(residue number reindexed from 1)		G109 S110 G111 K112 T113 T114 R139 K247 G272 T273 G274 E275
Annotation score3
Enzymatic activity
Enzyme Commision number 3.6.5.4: signal-recognition-particle GTPase.
Gene Ontology
Molecular Function
GO:0003723 RNA binding
GO:0003924 GTPase activity
GO:0005515 protein binding
GO:0005525 GTP binding
GO:0008312 7S RNA binding
GO:0016787 hydrolase activity
GO:0016887 ATP hydrolysis activity
GO:0019003 GDP binding
GO:0030942 endoplasmic reticulum signal peptide binding
GO:0043021 ribonucleoprotein complex binding
Biological Process
GO:0006614 SRP-dependent cotranslational protein targeting to membrane
GO:0006616 SRP-dependent cotranslational protein targeting to membrane, translocation
GO:0006617 SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition
GO:0030593 neutrophil chemotaxis
GO:0030851 granulocyte differentiation
GO:0031017 exocrine pancreas development
GO:0045047 protein targeting to ER
Cellular Component
GO:0005634 nucleus
GO:0005730 nucleolus
GO:0005737 cytoplasm
GO:0005783 endoplasmic reticulum
GO:0005786 signal recognition particle, endoplasmic reticulum targeting
GO:0005829 cytosol
GO:0016607 nuclear speck
GO:0048500 signal recognition particle

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:7nfx, PDBe:7nfx, PDBj:7nfx
PDBsum7nfx
PubMed34020957
UniProtP61011|SRP54_HUMAN Signal recognition particle subunit SRP54 (Gene Name=SRP54)

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