Structure of PDB 4zcl Chain A Binding Site BS01

Receptor Information
>4zcl Chain A (length=561) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MIEKLRNIAIIAHVDHGKTTLVDKLLQQSGTILAKNTAIKWNDYRINIVD
TPGHADFGGEVERVMSMVDSVLLVVDAFDGPMPQTRFVTKKAFAYGLKPI
VVINKVDRPGARPDWVVDQVFDLFVNLDATDEQLDFPIVYASALNGIAGL
DHEDMAEDMTPLYQAIVDHVPAPDVDLDGPFQMQISQLDYNSYVGVIGIG
RIKRGKVKPNQQVTIIDSEGKTRNAKVGKVLGHLGLERIETDLAEAGDIV
AITGLGELNISDTVCDTQNVEALPALSVDEPTVSMFFCVNTSPFCGKEGK
FVTSRQILDRLNKELVHNVALRVEETEDADAFRVSGRGELHLSVLIENMR
REGFELAVSRPKVIFREIDGRKQEPYENVTLDVEEQHQGSVMQALGERKG
DLKNMNPDGKGRVRLDYVIPSRGLIGFRSEFMTMTSGTGLLYSTFSHYDD
VRPGEVGQRQNGVLISNGQGKAVAFALFGLQDRGKLFLGHGAEVYEGQII
GIHSRSNDLTVNCLTVLVPPIRMTLEQALEFIDDDELVEVTPTSIRIRKR
HLTENDRRRAN
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 chain4zcl Chain A Residue 1003 [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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PDB4zcl Structural and Functional Analysis of BipA, a Regulator of Virulence in Enteropathogenic Escherichia coli.
Resolution3.06 Å
Binding residue
(original residue number in PDB)		D15 G17 K18 T19 T20 K129 D131 S166 L168
Binding residue
(residue number reindexed from 1)		D15 G17 K18 T19 T20 K105 D107 S142 L144
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) D15 K18 T19 H78
Catalytic site (residue number reindexed from 1) D15 K18 T19 H54
Enzyme Commision number 3.6.5.-
Gene Ontology
Molecular Function
GO:0000049 tRNA binding
GO:0003924 GTPase activity
GO:0005525 GTP binding
GO:0016787 hydrolase activity
GO:0019843 rRNA binding
GO:0043022 ribosome binding
GO:0097216 guanosine tetraphosphate binding
Biological Process
GO:0000027 ribosomal large subunit assembly
GO:0005975 carbohydrate metabolic process
GO:0042254 ribosome biogenesis
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:1990904 ribonucleoprotein complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4zcl, PDBe:4zcl, PDBj:4zcl
PDBsum4zcl
PubMed26163516
UniProtP0A3B2|BIPA_ECO27 Large ribosomal subunit assembly factor BipA (Gene Name=bipA)

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