Structure of PDB 4be7 Chain D Binding Site BS01

Receptor Information
>4be7 Chain D (length=835) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NFIVLDKYIKAEPTGDSYQSESDLERELIQDLRNQGYEFISVKSQSAMLA
NVREQLQNLNGVVFNDSEWRRFTEQYLDNPSDGILDKTRKIHIDYICDFI
FDDERLENIYLIDKKNLMRNKVQIIQQFRYDVTILVNGLPLVQIELKKRG
VAIREAFNQINSENSLFKYLQLFVISNGTDTRYFANTTKRDRNSFDFTMN
WAKSDNTLIKDLKDFTATCFQKHTLLNVLVNYSVFDSSQTLLVMRPYQIA
ATERILWKIKSSFTAKNWSKPESGGYIWHTTGSGKTLTSFKAARLATELD
FIDKVFFVVDRKDLDYQTMKEYQRFSPDSVNGSENTAGLKRNLDKDDNKI
IVTTIQKLNNLMKAESDLPVYNQQVVFIFDECHRSQFGEAQKNLKKKFKR
YYQFGFTGTPIFPENALGSETTASVFGRELHSYVITDAIRDEKVLKFKVD
YNDVRPQFKSLETETDEKKLSAAENQQAFLHPMRIQEITQYILNNFRQKT
HRTFPGSKGFNAMLAVSSVDAAKAYYATFKRLQEEAANKSATYKPLRIAT
IFSFAGEISDETFDTSAMDSSAKEFLDAAIREYNSHFKTNFSTDSNGFQN
YYRDLAQRVKNQDIDLLIVVGMFLTGFDAPTLNTLFVDKNLRYHGLMQAF
SRTNRIYDATKTFGNIVTFRDLERSTIDAITLFGDKNTKNVVLEKSYTEY
MEGFTDAATGEAKRGFMTVVSELEQRFPDPTSIESEKEKKDFVKLFGEYL
RAENILQNYDEFATLKALQQIDLSDPVAVEKFKAEHYVDDEKFAELQTIR
LPADRKIQDYRSAYNDIRDWQRRDDVVFEVDLLKS
Ligand information
Ligand IDATP
InChIInChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyZKHQWZAMYRWXGA-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
FormulaC10 H16 N5 O13 P3
NameADENOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL14249
DrugBankDB00171
ZINCZINC000004261765
PDB chain4be7 Chain D Residue 1887 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB4be7 Functional Coupling of Duplex Translocation to DNA Cleavage in a Type I Restriction Enzyme.
Resolution2.744 Å
Binding residue
(original residue number in PDB)		R220 L270 V271 R273 Q276 T309 G310 G312 K313 T314 L315 D664 R688 R691
Binding residue
(residue number reindexed from 1)		R192 L242 V243 R245 Q248 T281 G282 G284 K285 T286 L287 D628 R652 R655
Annotation score4
Enzymatic activity
Enzyme Commision number 3.1.21.3: type I site-specific deoxyribonuclease.
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0004519 endonuclease activity
GO:0005524 ATP binding
GO:0009035 type I site-specific deoxyribonuclease activity
Biological Process
GO:0006304 DNA modification
GO:0009307 DNA restriction-modification system

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:4be7, PDBe:4be7, PDBj:4be7
PDBsum4be7
PubMed26039067
UniProtP10486|T1R1_ECOLX Type I restriction enzyme EcoR124I/EcoR124II endonuclease subunit (Gene Name=hsdR)

[Back to BioLiP]