1EBM: Human 8-oxoguanine glycosylase

Crystal structure of the human 8-oxoguanine glycosylase (HOGG1) bound to a substrate oligonucleotide. Determined by X-ray diffraction at 2.1 Å resolution. Released 20 Mar 2000.

Method: X-ray diffraction
Resolution: 2.1 Å
Organism: Homo sapiens
Chains: 3
Atoms: 3,183
Mol. weight: 44.88 kDa
Ligands: CA
Released: 20 Mar 2000

Explore 1EBM in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1EBM contains 19 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: 19 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	20-22	3
β-strand	24-27	4	1
α-helix	35-38	4
β-strand	48-51	4	1
β-strand	54-58	5	1
β-strand	63-68	6	1
β-strand	72-78	7	1
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	221-227	7
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
DNA (5'-D(GPCPGPTPCPCPAP(8OG)PGPTPCPTPAPCP*C)-3')	C	DNA	15
DNA (5'-d(gpgptpapgpapcpcptpgpgpapcpgp*c)-3')	D	DNA	15
8-oxoguanine DNA glycosylase	A	protein	317	Homo sapiens	O15527 (AlphaFold model)

Sequence of entity 1 (C), FASTA

>1EBM_1 DNA (5'-D(*GP*CP*GP*TP*CP*CP*AP*(8OG)P*GP*TP*CP*TP*AP*CP*C)-3') (chains C)
GCGTCCAGGTCTACC

Sequence of entity 2 (D), FASTA

>1EBM_2 DNA (5'-D(*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*C)-3') (chains D)
GGTAGACCTGGACGC

Sequence of entity 3 (A), FASTA

>1EBM_3 8-OXOGUANINE DNA GLYCOSYLASE (chains A)
GSEGHRTLASTPALWASIPCPRSELRLDLVLPSGQSFRWREQSPAHWSGVLADQVWTLTQ
TEEQLHCTVYRGDKSQASRPTPDELEAVRKYFQLDVTLAQLYHHWGSVDSHFQEVAQKFQ
GVRLLRQDPIECLFSFICSSNNNIARITGMVERLCQAFGPRLIQLDDVTYHGFPSLQALA
GPEVEAHLRKLGLGYRARYVSASARAILEEQGGLAWLQQLRESSYEEAHKALCILPGVGT
QVADCICLMALDKPQAVPVDVHMWHIAQRDYSWHPTTSQAKGPSPQTNKELGNFFRSLWG
PYAGWAQAVLFSADLRQ

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	1

Primary citation

Structural basis for recognition and repair of the endogenous mutagen 8-oxoguanine in DNA. Bruner, S.D., Norman, D.P., Verdine, G.L. Nature (2000) 403:859-866. DOI 10.1038/35002510 · 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…
9NZ9 2.0 Å, Crystal structure of product-bound human OGG1(WT)
1LWY 2.01 Å, hOgg1 Borohydride-Trapped Intermediate without 8-oxoguanine

Browse structure collections

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