Structure of PDB 9bs3 Chain A Binding Site BS04

Receptor Information

>9bs3 Chain A (length=627) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

DPSGYNPAKNNYHPVEDACWKPGQKVPYLAVARTFEKIEEVSARLRMVET
LSNLLRSVVALSPPDLLPVLYLSLNHLGPPQQGLELGVGDGVLLKAVAQA
TGRQLESVRAEAAEKGDVGLVAENSRSPPPPLTASGVFSKFRDIARLTGS
ASTAKKIDIIKGLFVACRHSEARFIARSLSGRLRLGLAEQSVLAALSQAV
SLTPPGQEFPPAMVDAGKGKTAEARKTWLEEQGMILKQTFCEVPDLDRII
PVLLEHGLERLPEHCKLSPGIPLKPMLAHPTRGISEVLKRFEEAAFTCEY
KYDGQRAQIHALEGGEVKIFSRNQEDNTGKYPDIISRIPKIKLPSVTSFI
LDTEAVAWDREKKQIQPFQVLTTRKRKEVDASEIQVQVCLYAFDLIYLNG
ESLVREPLSRRRQLLRENFVETEGEFVFATSLDTKDIEQIAEFLEQSVKD
SCEGLMVKTLDVDATYEIAKRSHNWLKLKKDDTLDLVVIGAYLGRGKRAG
RYGGFLLASYDEDSEELQAICKLGTGFSDEELEEHHQSLKALVLPSPRPY
VRIDGAVIPDHWLDPSAVWEVKCADLSLSPIYPAARGLVDSDKGISLRFP
RFIRVREDKQPEQATTSAQVACLYRKQ

Ligand information

Ligand ID

AMP

InChI

InChI=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

InChIKey

UDMBCSSLTHHNCD-KQYNXXCUSA-N

SMILES

Software	SMILES
CACTVS 3.370	Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(O)=O)[CH](O)[CH]3O
CACTVS 3.370	Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.7.6	c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)N
ACDLabs 12.01	O=P(O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.7.6	c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)O)O)O)N

Formula

C10 H14 N5 O7 P

Name

ADENOSINE MONOPHOSPHATE

PDB chain

9bs3 Chain A Residue 1001 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

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Structure summary

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PDB	9bs3 Structures of LIG1 uncover the mechanism of sugar discrimination against 5'-RNA-DNA junctions during ribonucleotide excision repair.
Resolution	2.69 Å
Binding residue (original residue number in PDB)	E566 Y567 K568 Y569 E621 F660 E720 M723 K725 K744 K746
Binding residue (residue number reindexed from 1)	E299 Y300 K301 Y302 E354 F393 E453 M456 K458 K477 K479
Annotation score	4

External links

PDB	RCSB:9bs3, PDBe:9bs3, PDBj:9bs3
PDBsum	9bs3
PubMed	39159820
UniProt	P18858\|DNLI1_HUMAN DNA ligase 1 (Gene Name=LIG1)

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