Structure of PDB 8vdt Chain A Binding Site BS01

Receptor Information

>8vdt Chain A (length=635) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

LDPSGYNPAKNNYHPVEDACWKPGQKVPYLAVARTFEKIEEVSARLRMVE
TLSNLLRSVVALSPPDLLPVLYLSLNHLGPPQQGLALGVGDGVLLKAVAQ
ATGRQLESVRAEAAEKGDVGLVAENMLPPPPLTASGVFSKFRDIARLTGS
ASTAKKIDIIKGLFVACRHSEARFIARSLSGRLRLGLAEQSVLAALSQAV
SLTPPGQEFPPAMVDAGKGKTAEARKTWLEEQGMILKQTFCEVPDLDRII
PVLLEHGLERLPEHCKLSPGIPLKPMLAHPTRGISEVLKREAAFTCEYKY
DGQRAQIHALEGGEVKIFSRNQADNTGKYPDIISRIPKIKLPSVTSFILD
TEAVAWDREKKQIQPFQVLTTRKRKEVDASEIQVQVCLYAFDLIYLNGES
LVREPLSRRRQLLRENFVETEGEFVFATSLDTKDIEQIAEFLEQSVKDSC
EGLMVKTLDVDATYEIAKRNWLKLKKDYLDGVGDTLDLVVIGAYLGRGKR
AGRYGGFLLASYDEDSEELQAICKLGTGFSDEELEEHHQSLKALVLPSPR
PYVRIDGAVIPDHWLDPSAVWEVKCADLSLSPIYPAARGLVDSDKGISLR
FPRFIRVREDKQPEQATTSAQVACLYRKQSQIQNQ

Ligand information

>8vdt Chain B (length=18) [Search DNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

gctgatgcgtagtcggac

Receptor-Ligand Complex Structure

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Structure summary

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PDB	8vdt Structures of LIG1 provide a mechanistic basis for understanding a lack of sugar discrimination against a ribonucleotide at the 3'-end of nick DNA.
Resolution	2.78 Å
Binding residue (original residue number in PDB)	S303 G348 G350 K568 G571 Q572 R573 S588 A592 N594 F635 Y749 T798 G799 F800 S801 D802 F872 R874
Binding residue (residue number reindexed from 1)	S43 G88 G90 K299 G302 Q303 R304 S319 A323 N325 F366 Y478 T527 G528 F529 S530 D531 F601 R603

Enzymatic activity

Enzyme Commision number

6.5.1.1: DNA ligase (ATP).

External links

PDB	RCSB:8vdt, PDBe:8vdt, PDBj:8vdt
PDBsum	8vdt
PubMed	38522520
UniProt	P18858\|DNLI1_HUMAN DNA ligase 1 (Gene Name=LIG1)

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