Structure of PDB 6dt1 Chain E Binding Site BS04

Receptor Information
>6dt1 Chain E (length=459) Species: 10665 (Tequatrovirus T4) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MILKILNEIASIGSTKQKQAILEKNKDNELLKRVYRLTYSRGLQYYIKKW
PKPGIATQSFGMLTLTDMLDFIEFTLATRKLTGNAAIEELTGYITDGKKD
DVEVLRRVMMRDLECGASVSIANKVWPGLIPEQPQMLASSYDEKGINKNI
KFPAFAQLKADGARCFAEVRGDELDDVRLLSRAGNEYLGLDLLKEELIKM
TAEARQIHPEGVLIDGELVYHVAESRTASNGIANKSLKGTISEKEAQCMK
FQVWDYVPLVEIYSLPAFRLKYDVRFSKLEQMTSGYDKVILIENQVVNNL
DEAKVIYKKYIDQGLEGIILKNIDGLWENARSKNLYKFKEVIDVDLKIVG
IYPHRKDPTKAGGFILESECGKIKVNAGSGLKDKAGVKSHELDRTRIMEN
QNYYIGKILECECNGWLKSDGRTDYVKLFLPIAIRLREDKTKANTFEDVF
GDFHEVTGL
Ligand information
Ligand IDAMP
InChIInChI=1S/C10H14N5O7P/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(22-10)1-21-23(18,19)20/h2-4,6-7,10,16-17H,1H2,(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyUDMBCSSLTHHNCD-KQYNXXCUSA-N
SMILES
SoftwareSMILES
CACTVS 3.370Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(O)=O)[CH](O)[CH]3O
CACTVS 3.370Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.7.6c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)N
ACDLabs 12.01O=P(O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.7.6c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)O)O)O)N
FormulaC10 H14 N5 O7 P
NameADENOSINE MONOPHOSPHATE
ChEMBLCHEMBL752
DrugBankDB00131
ZINCZINC000003860156
PDB chain6dt1 Chain E Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6dt1 T4 DNA ligase structure reveals a prototypical ATP-dependent ligase with a unique mode of sliding clamp interaction.
Resolution2.75 Å
Binding residue
(original residue number in PDB)		Q157 L158 K159 A160 R164 E217 W282 I347 K349 K365 K367
Binding residue
(residue number reindexed from 1)		Q157 L158 K159 A160 R164 E217 W254 I319 K321 K337 K339
Annotation score4
Enzymatic activity
Enzyme Commision number 6.5.1.1: DNA ligase (ATP).
Gene Ontology
Molecular Function
GO:0003909 DNA ligase activity
GO:0003910 DNA ligase (ATP) activity
GO:0005524 ATP binding
GO:0016491 oxidoreductase activity
GO:0016874 ligase activity
GO:0046872 metal ion binding
Biological Process
GO:0006260 DNA replication
GO:0006281 DNA repair
GO:0006310 DNA recombination

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Molecular Function
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Biological Process
External links
PDB RCSB:6dt1, PDBe:6dt1, PDBj:6dt1
PDBsum6dt1
PubMed30169742
UniProtP00970|DNLI_BPT4 DNA ligase (Gene Name=30)

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