9NZ9: Product-bound human OGG1(WT)

Crystal structure of product-bound human OGG1(WT). Determined by X-ray diffraction at 2.0 Å resolution. Released 15 Apr 2026.

Method: X-ray diffraction
Resolution: 2.0 Å
Organisms: Homo sapiens, synthetic construct
Chains: 4
Atoms: 3,185
Mol. weight: 44.94 kDa
Released: 15 Apr 2026

Explore 9NZ9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9NZ9 contains 22 α-helices and 7 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 22 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	20-22	3
β-strand	24-27	4	1
α-helix	30-32	3
α-helix	35-38	4
β-strand	48-51	4	1
β-strand	54-59	6	1
β-strand	62-68	7	1
β-strand	72-78	7	1
α-helix	84-85	2
α-helix	87-89	3
α-helix	90-99	10
α-helix	106-116	11
α-helix	118-124	7
α-helix	137-145	9
α-helix	152-166	15
α-helix	168	1
β-strand	169-173	5	2
β-strand	176-179	4	2
α-helix	180-183	4
α-helix	184-187	4
α-helix	192-198	7
α-helix	204-217	14
α-helix	222-226	5
α-helix	227-229	3
α-helix	233-240	8
α-helix	248-258	11
α-helix	269-279	11
α-helix	293-307	15
α-helix	311-323	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
N-glycosylase/DNA lyase	A	protein	319	Homo sapiens	O15527 (AlphaFold model)
DNA (5'-d(ptpapgpapgptpcp(pua))-3')	C	DNA	8	synthetic construct
DNA (5'-d(papcpcptpgpc)-3')	B	DNA	7	synthetic construct
DNA (5'-d(tpgpcpapgpgptpcpgpapcptpcpt)-3')	D	DNA	15	synthetic construct

Sequence of entity 1 (A), FASTA

>9NZ9_1 N-glycosylase/DNA lyase (chains A)
SNAGHRTLASTPALWASIPCPRSELRLDLVLPSGQSFRWREQSPAHWSGVLADQVWTLTQ
TEEQLHCTVYRGDKSQASRPTPDELEAVRKYFQLDVTLAQLYHHWGSVDSHFQEVAQKFQ
GVRLLRQDPIECLFSFICSSNNNIARITGMVERLCQAFGPRLIQLDDVTYHGFPSLQALA
GPEVEAHLRKLGLGYRARYVSASARAILEEQGGLAWLQQLRESSYEEAHKALCILPGVGT
KVADCICLMALDKPQAVPVDVHMWHIAQRDYSWHPTTSQAKGPSPQTNKELGNFFRSLWG
PYAGWAQAVLFSADLRQSR

Sequence of entity 2 (C), FASTA

>9NZ9_2 DNA (5'-D(P*TP*AP*GP*AP*GP*TP*CP*(PUA))-3') (chains C)
TAGAGTCX

Sequence of entity 3 (B), FASTA

>9NZ9_3 DNA (5'-D(P*AP*CP*CP*TP*GP*C)-3') (chains B)
ACCTGCA

Sequence of entity 4 (D), FASTA

>9NZ9_4 DNA (5'-D(*TP*GP*CP*AP*GP*GP*TP*CP*GP*AP*CP*TP*CP*T)-3') (chains D)
TGCAGGTCGACTCTA

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. et al. Nat Commun (2026) 17. DOI 10.1038/s41467-026-75471-1 · PubMed

Other PDB entries of the same protein (UniProt O15527 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8XWC 1.45 Å, Crystal structure of human 8-oxoguanine glycosylase K249H mutant bound to the substrate…
2XHI 1.55 Å, Separation-of-function mutants unravel the dual reaction mode of human 8-oxoguanine DNA…
5AN4 1.6 Å, Crystal structure of the human 8-oxoguanine glycosylase (OGG1) processed with the…
8XWU 1.68 Å, Crystal structure of human 8-oxoguanine glycosylase K249H mutant bound to the reaction…
8XXK 1.7 Å, Crystal structure of human 8-oxoguanine glycosylase K249H mutant bound to the reaction…
8XXG 1.82 Å, Crystal structure of human 8-oxoguanine glycosylase K249H mutant bound to the reaction…
9NZ8 1.85 Å, Crystal structure of human OGG1 in a DNA-free state
1M3Q 1.9 Å, Crystal Structure of hogg1 D268E Mutant with Base-Excised DNA and 8-aminoguanine
6RLW 2.0 Å, Structure of the human 8-oxoguanine DNA Glycosylase hOGG1 in complex with inhibitor TH5487
7AYY 2.0 Å, Structure of the human 8-oxoguanine DNA Glycosylase hOGG1 in complex with activator…
1LWY 2.01 Å, hOgg1 Borohydride-Trapped Intermediate without 8-oxoguanine
2NOH 2.01 Å, Structure of catalytically inactive Q315A human 8-oxoguanine glycosylase complexed to…

Browse structure collections

About this viewer

MolViewer shows 9NZ9 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.