Structure of PDB 8vdt Chain A

Receptor sequence

>8vdtA (length=635) Species: 9606 (Homo sapiens)

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

3D structure

• 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.
• Chain: A
• Resolution: 2.78 Å

Enzymatic activity

• Enzyme Commision number: 6.5.1.1: DNA ligase (ATP).

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	dna	A	S303 G348 G350 K568 G571 Q572 R573 S588 A592 N594 F635 Y749 T798 G799 F800 S801 D802 F872 R874	S43 G88 G90 K299 G302 Q303 R304 S319 A323 N325 F366 Y478 T527 G528 F529 S530 D531 F601 R603
BS02	dna	A	R305 T415 G416 A418 T420 R451 G453 A455 Q457 S458 Q636 T639 R641 K642 R643 R768 G769 K770 G776 C794 K795 G797 S850 S852 P853 Y855 S869 L870	R45 T148 G149 A151 T153 R184 G186 A188 Q190 S191 Q367 T370 R372 K373 R374 R497 G498 K499 G505 C523 K524 G526 S579 S581 P582 Y584 S598 L599

External links

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