Structure of PDB 4beb Chain D Binding Site BS02

Receptor Information
>4beb Chain D (length=833) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NFIVLDKYIKAEPTGDSYQSESDLERELIQDLRNQGYEFISVKSQSAMLA
NVREQLQNLNGVVFNDSEWRRFTEQYLDNPSDGILDKTRKIHIDYICDFI
FDDERLENIYLIDKKNLMRNKVQIIQQFRYDVTILVNGLPLVQIELKKRG
VAIREAFNQINSLFKYLQLFVISNGTDTRYFANTTKRDENSFDFTMNWAK
SDNTLIKDLKDFTATCFQKHTLLNVLVNYSVFDSSQTLLVMRPYQIAATE
RILWKIKSSFTAKNWSKPESGGYIWHTTGSGKTLTSFKAARLATELDFID
KVFFVVDRKDLDYQTMKEYQRFSPDSVNGSENTAGLKRNLDKDDNKIIVT
TIQKLNNLMKAESDLPVYNQQVVFIFDECHRSQFGEAQKNLKKKFKRYYQ
FGFTGTPIFPENALGSETTASVFGRELHSYVITDAIRDEKVLKFKVDYND
VRPQFKSLETETDEKKLSAAENQQAFLHPMRIQEITQYILNNFRQKTHRT
FPGSKGFNAMLAVSSVDAAKAYYATFKRLQEEAANKSATYKPLRIATIFS
FAEISDETFDTSAMDSSAKEFLDAAIREYNSHFKTNFSTDSNGFQNYYRD
LAQRVKNQDIDLLIVVGMFLTGFDAPTLNTLFVDKNLRYHGLMQAFSRTN
RIYDATKTFGNIVTFRDLERSTIDAITLFGDKNTKNVVLEKSYTEYMEGF
TDAATGEAKRGFMTVVSELEQRFPDPTSIESEKEKKDFVKLFGEYLRAEN
ILQNYDEFATLKALQQIDLSDPVAVEKFKAEHYVDDEKFAELQTIRLPAD
RKIQDYRSAYNDIRDWQRRTDWDDVVFEVDLLK
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 chain4beb Chain D Residue 1886 [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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PDB4beb Functional Coupling of Duplex Translocation to DNA Cleavage in a Type I Restriction Enzyme.
Resolution2.989 Å
Binding residue
(original residue number in PDB)		M227 V271 R273 Q276 G312 K313 T314 T661 D664 R688 R691
Binding residue
(residue number reindexed from 1)		M196 V240 R242 Q245 G281 K282 T283 T621 D624 R648 R651
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:4beb, PDBe:4beb, PDBj:4beb
PDBsum4beb
PubMed26039067
UniProtP10486|T1R1_ECOLX Type I restriction enzyme EcoR124I/EcoR124II endonuclease subunit (Gene Name=hsdR)

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