Structure of PDB 6ut6 Chain D Binding Site BS02

Receptor Information
>6ut6 Chain D (length=292) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TESYCLEDALNDLFIPETTIETILKRLTIKKNIILQGPPGVGKTFVARRL
AYLLTGEKAPQRVNMVQFHQSYSYEDFIQGYRPNGVGFRRKDGIFYNFCQ
QAKEQPEKKYIFIIDEINRANLSKVFGEVMMLMEHDKRGENWSVPLTYSE
NDEERFYVPENVYIIGLMNTADRSLAVVDYALRRRFSFIDIEPGFDTPQF
RNFLLNKKAEPSFVESLCQKMNELNQEISKEATILGKGFRIGHSYFCCGL
EDGTSPDTQWLNEIVMTDIAPLLEEYFFDDPYKQQKWTNKLL
Ligand information
Ligand IDGSP
InChIInChI=1S/C10H16N5O13P3S/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(26-9)1-25-29(19,20)27-30(21,22)28-31(23,24)32/h2-3,5-6,9,16-17H,1H2,(H,19,20)(H,21,22)(H2,23,24,32)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
InChIKeyXOFLBQFBSOEHOG-UUOKFMHZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=S)(O)O)O)O)N=C(NC2=O)N
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=S)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@](=O)(O)OP(=S)(O)O)O)O)N=C(NC2=O)N
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=S)[CH](O)[CH]3O
ACDLabs 10.04S=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
FormulaC10 H16 N5 O13 P3 S
Name5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE
ChEMBLCHEMBL1204628
DrugBankDB01864
ZINCZINC000008217391
PDB chain6ut6 Chain D Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6ut6 Structural asymmetry governs the assembly and GTPase activity of McrBC restriction complexes
Resolution3.28 Å
Binding residue
(original residue number in PDB)		D176 L177 F178 G204 V205 G206 K207 T208 F209 N333 H407 S408
Binding residue
(residue number reindexed from 1)		D12 L13 F14 G40 V41 G42 K43 T44 F45 N169 H243 S244
Annotation score3
Enzymatic activity
Enzyme Commision number 3.1.21.-
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0003924 GTPase activity
GO:0004519 endonuclease activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0005525 GTP binding
GO:0010385 double-stranded methylated DNA binding
GO:0016887 ATP hydrolysis activity
GO:0042802 identical protein binding
GO:0044729 hemi-methylated DNA-binding
Biological Process
GO:0009307 DNA restriction-modification system
Cellular Component
GO:1905348 endonuclease complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6ut6, PDBe:6ut6, PDBj:6ut6
PDBsum6ut6
PubMed33219217
UniProtP15005|MCRB_ECOLI Type IV methyl-directed restriction enzyme EcoKMcrB subunit (Gene Name=mcrB)

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