Structure of PDB 3dm5 Chain A Binding Site BS01

Receptor Information
>3dm5 Chain A (length=416) Species: 2261 (Pyrococcus furiosus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MVLDNLGKALANTLKKIARASSVDEALIKELVRDIQRALIQADVNVRLVL
QLTREIQRRALEEKPPAGISKKEHIIKIVYEELTKFLGTEAKPIEIKEKP
TILLMVGIQGSGKTTTVAKLARYFQKRGYKVGVVCSDTWRPGAYHQLRQL
LDRYHIEVFGNPQEKDAIKLAKEGVDYFKSKGVDIIIVDTAGRHKEDKAL
IEEMKQISNVIHPHEVILVIDGTIGQQAYNQALAFKEATPIGSIIVTKLD
GSAKGGGALSAVAATGAPIKFIGTGEKIDDIEPFDPPRFVSRLLGLGDIQ
GLLEKFKELEKEVEIKEEDIERFLRGKFTLKDMYAQLEAMRKMGPISIGE
ERLKKFKVIMDSMTEEELLNPEIINYSRIKRIARGSGTSTKDVKELLDQY
RQMKKLFKSMNKRQLS
Ligand information
Ligand IDGDP
InChIInChI=1S/C10H15N5O11P2/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(25-9)1-24-28(22,23)26-27(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
InChIKeyQGWNDRXFNXRZMB-UUOKFMHZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
CACTVS 3.385NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
CACTVS 3.385NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
OpenEye OEToolkits 1.7.6c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
FormulaC10 H15 N5 O11 P2
NameGUANOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL384759
DrugBankDB04315
ZINCZINC000008215481
PDB chain3dm5 Chain A Residue 501 [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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PDB3dm5 Structures of SRP54 and SRP19, the two proteins that organize the ribonucleic core of the signal recognition particle from Pyrococcus furiosus.
Resolution2.51 Å
Binding residue
(original residue number in PDB)		G110 S111 G112 K113 T114 T115 R140 K248 D250 G273 G275 E276
Binding residue
(residue number reindexed from 1)		G110 S111 G112 K113 T114 T115 R140 K248 D250 G273 G275 E276
Annotation score4
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:0005525 GTP binding
GO:0008312 7S RNA binding
GO:0016787 hydrolase activity
GO:0016887 ATP hydrolysis activity
Biological Process
GO:0006612 protein targeting to membrane
GO:0006614 SRP-dependent cotranslational protein targeting to membrane
Cellular Component
GO:0005737 cytoplasm
GO:0048500 signal recognition particle

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3dm5, PDBe:3dm5, PDBj:3dm5
PDBsum3dm5
PubMed18953414
UniProtQ8U070|SRP54_PYRFU Signal recognition particle 54 kDa protein (Gene Name=srp54)

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