Structure of PDB 6xrs Chain C Binding Site BS01

Receptor Information
>6xrs Chain C (length=388) Species: 521006 (Neisseria gonorrhoeae NCCP11945) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKPTIALIGRPNVGKSTLFNRLTRDLPGLTRDRHYGHGKVGSKPYFVIDT
GGFEHEMAKQTLQAVDEADAVVFLVDGRTGLTPQDKIIADRLRQSPRPVY
LAVNKGEGGDRAVLAAEFYELALGEPHVISGAHGDGVYYLIEEILENFPE
ADAKHPVFAVIGRPNVGKSTLVNAILGEKRVIAFIHIDFEREGKPFTIID
TFSVIKAMQAVEAANVAVLVLDAQQDIADQDATIAGFALEAGRALVVAVN
KWDGISEERREQVKRDISRKLYFLDFAKFHFISALKERGIDGLFESIQAA
YNAAMIKMPTPKITRVLQTAVGRQQPPRAGLVRPKMRYAHQGGMNPPVIV
VHGNSLHAISDSYTRYLTQTFRKAFNLQGTPLRIQYNV
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 chain6xrs Chain C 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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PDB6xrs Crystal structure of a GTP-binding protein EngA (Der homolog) from Neisseria gonorrhoeae bound to GDP
Resolution2.8 Å
Binding residue
(original residue number in PDB)		N27 G29 K30 S31 T32 K135 E137 A162
Binding residue
(residue number reindexed from 1)		N12 G14 K15 S16 T17 K105 E107 A132
Annotation score3
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0005525 GTP binding
GO:0016887 ATP hydrolysis activity
GO:0043022 ribosome binding
Biological Process
GO:0000027 ribosomal large subunit assembly
GO:0042254 ribosome biogenesis

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:6xrs, PDBe:6xrs, PDBj:6xrs
PDBsum6xrs
PubMed
UniProtB4RKD2|DER_NEIG2 GTPase Der (Gene Name=der)

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