ISDA: 9NZD

Deposition Date 2025-03-31

Release Date 2026-04-15

Last Version Date 2026-08-26

Entry Detail

PDB ID:

9NZD

Keywords:

LYASE/DNA

Title:

Crystal structure of AfNth1-K122A mutant bound to Tg-DNA duplex complex in an intermediate state

Biological Source:

Source Organism(s):

Archaeoglobus fulgidus (Taxon ID: 2234)
synthetic construct (Taxon ID: 32630)

Expression System(s):

Escherichia coli

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

3.10 Å

R-Value Free:

0.26

R-Value Work:

0.21

R-Value Observed:

0.21

Space Group:

P 41 21 2

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Macromolecular Entities

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Endonuclease III
Gene (Uniprot):nth
Mutagens:K122A
Chain IDs:A, D
Chain Length:209
Number of Molecules:2
Biological Source:Archaeoglobus fulgidus

UniProt ID:O28581 Pfam ID:PF00730, PF00633, PF10576 EC:4.2.99.18

Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(*TP*TP*GP*GP*CP*GP*
Chain IDs:B, E
Chain Length:13
Number of Molecules:2
Biological Source:synthetic construct

Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(*AP*CP*GP*CP*GP*AP*
Chain IDs:C, F
Chain Length:13
Number of Molecules:2
Biological Source:synthetic construct

Ligand Molecules

SF4

Primary Citation

A unified catalytic mechanism in bifunctional DNA glycosylases with an evolutionarily conserved aspartate-lysine dyad.

Syed, A, Serafim, L.F, Arvai, A.S, Minko, I.G, Tang, H.Y.H, Huffman, J.L, Mol, C.D, Hitomi, K, Sarker, A.H, Parikh, S, Tsai, C.L, Bacolla, A, Shin, D.S, Cunningham, R.P, Iwai, S, Chowdhury, D, Lloyd, R.S, Ivanov, I, Tainer, J.A.Show

Nat Commun 17 ? ? (2026)

PMID: 42457729 DOI: 10.1038/s41467-026-75471-1

Primary Citation of related structures

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