6RLW: Human 8-oxoguanine DNA Glycosylase hOGG1

Structure of the human 8-oxoguanine DNA Glycosylase hOGG1 in complex with inhibitor TH5487. Determined by X-ray diffraction at 2.0 Å resolution. Released 22 Jul 2020.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Homo sapiens
Chains: 5
Atoms: 13,184
Mol. weight: 192.32 kDa
Ligands: K8Q
Released: 22 Jul 2020

Explore 6RLW in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6RLW contains 101 α-helices and 35 β-strands across 5 chains. 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 AAA: 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	54-59	6	1
β-strand	62-68	7	1
β-strand	72-78	7	1
α-helix	84-85	2
α-helix	90-99	10
α-helix	106-116	11
α-helix	118-126	9
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	184-188	5
α-helix	192-198	7
α-helix	204-218	15
α-helix	223-230	8
α-helix	233-240	8
α-helix	248-258	11
α-helix	269-279	11
α-helix	293-307	15
α-helix	311-324	14

Chain BBB: 20 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	20-22	3
β-strand	24-27	4	3
α-helix	35-38	4
β-strand	47-51	5	3
β-strand	54-59	6	3
β-strand	62-68	7	3
β-strand	72-78	7	3
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	4
β-strand	176-179	4	4
α-helix	180-183	4
α-helix	184-187	4
α-helix	192-198	7
α-helix	204-214	11
α-helix	215-219	5
α-helix	223-230	8
α-helix	233-240	8
α-helix	248-258	11
α-helix	269-278	10
α-helix	293-307	15
α-helix	311-323	13

Chain CCC: 21 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	12-14	3
α-helix	20-22	3
β-strand	24-27	4	5
α-helix	35-38	4
β-strand	48-51	4	5
β-strand	54-58	5	5
β-strand	63-68	6	5
β-strand	72-78	7	5
α-helix	83-85	3
α-helix	87-89	3
α-helix	90-99	10
α-helix	106-114	9
α-helix	118-126	9
α-helix	137-145	9
α-helix	152-166	15
α-helix	168	1
β-strand	169-173	5	6
β-strand	176-179	4	6
α-helix	180-183	4
α-helix	184-187	4
α-helix	192-198	7
α-helix	204-217	14
α-helix	222-230	9
α-helix	233-240	8
α-helix	248-258	11
α-helix	269-279	11
α-helix	293-307	15
α-helix	311-322	12

Chain DDD: 21 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	20-22	3
β-strand	24-27	4	7
α-helix	35-38	4
β-strand	47-51	5	7
β-strand	54-59	6	7
β-strand	62-68	7	7
β-strand	72-78	7	7
α-helix	83-85	3
α-helix	90-99	10
α-helix	106-115	10
α-helix	118-126	9
α-helix	131-133	3
α-helix	137-145	9
α-helix	152-166	15
α-helix	168	1
β-strand	169-173	5	8
β-strand	176-179	4	8
α-helix	180-183	4
α-helix	184-187	4
α-helix	192-198	7
α-helix	204-214	11
α-helix	215-219	5
α-helix	223-229	7
α-helix	233-240	8
α-helix	248-258	11
α-helix	269-279	11
α-helix	293-307	15
α-helix	311-321	11

Chain EEE: 20 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	20-22	3
β-strand	24-27	4	9
α-helix	35-37	3
β-strand	48-51	4	9
β-strand	54-59	6	9
β-strand	62-68	7	9
β-strand	72-78	7	9
α-helix	87-89	3
α-helix	90-99	10
α-helix	106-116	11
α-helix	118-126	9
α-helix	137-145	9
α-helix	152-166	15
α-helix	168	1
β-strand	169-173	5	10
β-strand	176-179	4	10
α-helix	180-183	4
α-helix	184-187	4
α-helix	192-198	7
α-helix	204-214	11
α-helix	215-219	5
α-helix	223-230	8
α-helix	233-240	8
α-helix	248-257	10
α-helix	269-278	10
α-helix	293-307	15
α-helix	311-324	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
N-glycosylase/DNA lyase	AAA, BBB, CCC, DDD, EEE	protein	337	Homo sapiens	O15527 (AlphaFold model)

Sequence of entity 1 (AAA, BBB, CCC, DDD, EEE), FASTA

>6RLW_1 N-glycosylase/DNA lyase (chains AAA, BBB, CCC, DDD, EEE)
MGSSHHHHHHSSGLVPRGSHMGHRTLASTPALWASIPCPRSELRLDLVLPSGQSFRWREQ
SPAHWSGVLADQVWTLTQTEEQLHCTVYRGDKSQASRPTPDELEAVRKYFQLDVTLAQLY
HHWGSVDSHFQEVAQKFQGVRLLRQDPIECLFSFICSSNNNIARITGMVERLCQAFGPRL
IQLDDVTYHGFPSLQALAGPEVEAHLRKLGLGYRARYVSASARAILEEQGGLAWLQQLRE
SSYEEAHKALCILPGVGTKVADCICLMALDKPQAVPVDVHMWHIAQRDYSWHPTTSQAKG
PSPQTNKELGNFFRSLWGPYAGWAQAVLFSADLRQSR

Ligands and cofactors

ID	Name	Formula	Copies
K8Q	4-(4-bromanyl-2-oxidanylidene-3~{H}-benzimidazol-1-yl)-~{N}-(4-iodophenyl)piper…	C19 H18 Br I N4 O2	5

Primary citation

Targeting OGG1 arrests cancer cell proliferation by inducing replication stress. Visnes, T., Benitez-Buelga, C., Cazares-Korner, A. et al. Nucleic Acids Res (2020) 48:12234-12251. DOI 10.1093/nar/gkaa1048 · 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
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
2NOH 2.01 Å, Structure of catalytically inactive Q315A human 8-oxoguanine glycosylase complexed to…

Browse structure collections

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