Structure of PDB 8vds Chain A Binding Site BS01

Receptor Information

>8vds Chain A (length=640) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

LDPSGYNPAKNNYHPVEDACWKPGQKVPYLAVARTFEKIEEVSARLRMVE
TLSNLLRSVVALSPPDLLPVLYLSLNHLGPPQQGLALGVGDGVLLKAVAQ
ATGRQLESVRAEAAEKGDVGLVAENLMLPPPPLTASGVFSKFRDIARLTG
SASTAKKIDIIKGLFVACRHSEARFIARSLSGRLRLGLAEQSVLAALSQA
VSLTPPGQEFPPAMVDAGKGKTAEARKTWLEEQGMILKQTFCEVPDLDRI
IPVLLEHGLERLPEHCKLSPGIPLKPMLAHPTRGISEVLKRFEEAAFTCE
YKYDGQRAQIHALEGGEVKIFSRNQADNTGKYPDIISRIPKIKLPSVTSF
ILDTEAVAWDREKKQIQPFQVLTTRKRKEVDASEIQVQVCLYAFDLIYLN
GESLVREPLSRRRQLLRENFVETEGEFVFATSLDTKDIEQIAEFLEQSVK
DSCEGLMVKTLDVDATYEIAKRSHNWLKLKKDYLDGVGDTLDLVVIGAYL
GRGKRAGRYGGFLLASYDEDSEELQAICKLGTGFSDEELEEHHQSLKALV
LPSPRPYVRIDGAVIPDHWLDPSAVWEVKCADLSLSPIYPAARGLVDSDK
GISLRFPRFIRVREDKQPEQATTSAQVACLYRKQSQIQNQ

Ligand information

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

gctgatgcgtggtcggac

Receptor-Ligand Complex Structure

Global view

Local view

Structure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]

PDB	8vds 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	2.79 Å
Binding residue (original residue number in PDB)	S303 G348 G350 G571 R573 S588 N594 F635 R643 Y749 T798 F800 S801 D802 F872 R874
Binding residue (residue number reindexed from 1)	S43 G88 G90 G305 R307 S322 N328 F369 R377 Y483 T532 F534 S535 D536 F606 R608

Enzymatic activity

Enzyme Commision number

6.5.1.1: DNA ligase (ATP).

External links

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

[Back to BioLiP]