Structure of PDB 4w2e Chain y Binding Site BS04

Receptor Information
>4w2e Chain y (length=644) Species: 300852 (Thermus thermophilus HB8) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKVILLEPLENLGDVGQVVDVKPGYARNYLLPRGLAVLATESNLKALEAR
IRAQAKRLAERKAEAERLKEILENLSRIRNFSIIAHVDHGKSTLADRILE
LTHSAVRVTYRAKDGEEYVFHLIDTPGHVDFTYEVSRALAAVEGVLLVVD
ASQGVEAETLAKFYMALEHGHVIIPVINKIDLPNARPLEVALEVEEVLGL
PADEAIFASGKTGEGVEEILEAIVQRIPPPKGDPEAPLKALIFDSVYDAY
QGVIPYLRLFEGRVRPGDRIRIYSTGKEFTVDKVGVFTPQGLVATEALEA
GEVGWLVAAIRDIHDVQVGDTITLADRPTPSPYPGFRPAKPVVFAGLYPV
DSGDYGKLRDALEKLKLNDAALTFEPESSTALGFGFRCGFLGLLHAEIVQ
ERLEREFGLSLIATAPSVVYKVRLKSGEEVEVHNPADLPDPTRIEEILEP
YVKLTIFTPEEYVGSLMQLLQEKRGRLVNMNYLPGAQKRVELVYEAPFAE
ILYDFHDRLKSVSRGYASMDYEQAGYRPGDLVKVNVLVHGEVVDALTFIA
HREKAYTMARAIVDKLAEVIPRQLFEVPIQAAIGGKIIARATVKALRKDV
LAKCYGGDVTRKKKLLEKQKEGKKRLKAIGKVEVPQEAFLAVLS
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 chain4w2e Chain y Residue 703 [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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PDB4w2e Crystal structure of elongation factor 4 bound to a clockwise ratcheted ribosome.
Resolution2.9 Å
Binding residue
(original residue number in PDB)		V18 D19 K22 S23 T24 K137 L140 G168 K169
Binding residue
(residue number reindexed from 1)		V87 D88 K91 S92 T93 K179 L182 G210 K211
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) K22 S23 H86
Catalytic site (residue number reindexed from 1) K91 S92 H128
Enzyme Commision number ?
3.6.5.n1: elongation factor 4.
Gene Ontology
Molecular Function
GO:0003735 structural constituent of ribosome
GO:0003746 translation elongation factor activity
GO:0003924 GTPase activity
GO:0005525 GTP binding
GO:0016787 hydrolase activity
GO:0043022 ribosome binding
Biological Process
GO:0006412 translation
GO:0006414 translational elongation
GO:0045727 positive regulation of translation
Cellular Component
GO:0005840 ribosome
GO:0005886 plasma membrane

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:4w2e, PDBe:4w2e, PDBj:4w2e
PDBsum4w2e
PubMed25104389
UniProtQ5SKA7|LEPA_THET8 Elongation factor 4 (Gene Name=lepA);
Q5SLQ1|RL9_THET8 Large ribosomal subunit protein bL9 (Gene Name=rplI)

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