Structure of PDB 6xrs Chain A Binding Site BS01

Receptor Information
>6xrs Chain A (length=388) Species: 521006 (Neisseria gonorrhoeae NCCP11945) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IMKPTIALIGRPNVGKSTLFNRLTRTKDALVHDLPGLTRDRHYGHGKVGS
KPYFVIDTGGFEMAKQTLQAVDEADAVVFLVDGRTGLTPQDKIIADRLRQ
SPRPVYLAVNKGEDRAVLAAEFYELALGEPHVISGAHGDGVYYLIEEILE
NFPEADAKHPVFAVIGRPNVGKSTLVNAILGEKRVIASIHIDFEREGKPF
TIIDKFSVIKAMQAVEAANVAVLVLDAQQDIADQDATIAGFALEAGRALV
VAVNKWDGISEERREQVKRDISRKLYFLDFAKFHFISALKERGIDGLFES
IQAAYNAAMIKMPTPKITRVLQTAVGRQQPPVRPKMRYAHQGGMNPPVIV
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 A 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)		N200 G202 K203 S204 T205 N309 K310 D312 S342 L344
Binding residue
(residue number reindexed from 1)		N169 G171 K172 S173 T174 N254 K255 D257 S287 L289
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

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Molecular Function
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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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