SAXSdb — 6rlw

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1. Protein Identity and Related Structures Protein Identity & Related Structures

N-glycosylase/DNA lyase

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	4-(4-bromanyl-2-oxidanylidene-3~{H}-benzimidazol-1-yl)-~{N}-(4-iodophenyl)piperidine-1-carboxamide × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	4-(4-bromanyl-2-oxidanylidene-3~{H}-benzimidazol-1-yl)-~{N}-(4-iodophenyl)piperidine-1-carboxamide × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	4-(4-bromanyl-2-oxidanylidene-3~{H}-benzimidazol-1-yl)-~{N}-(4-iodophenyl)piperidine-1-carboxamide × 1 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	4-(4-bromanyl-2-oxidanylidene-3~{H}-benzimidazol-1-yl)-~{N}-(4-iodophenyl)piperidine-1-carboxamide × 1 water × 1	Consistent with protein count
5	Protein monomer	Monomer	Protein 1	4-(4-bromanyl-2-oxidanylidene-3~{H}-benzimidazol-1-yl)-~{N}-(4-iodophenyl)piperidine-1-carboxamide × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	OGG1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain AAA； PDBConstruct 21–337； UniProt 11–327 Author chain BBB； PDBConstruct 21–337； UniProt 11–327 Author chain CCC； PDBConstruct 21–337； UniProt 11–327 Author chain DDD； PDBConstruct 21–337； UniProt 11–327 Author chain EEE； PDBConstruct 21–337； UniProt 11–327

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	6rlw
Deposition date deposition_date	2019-05-03
Structure title title	Structure of the human 8-oxoguanine DNA Glycosylase hOGG1 in complex with inhibitor TH5487
Keywords keywords	DNA repair, cancer, small molecule inhibitor, DNA BINDING PROTEIN; DNA BINDING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

6rlw__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

6rlw__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6rlw__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	20.64 Å
Rg (electron density)	19.54 Å
Total Rg	20.36 Å
Atom count	2523
Residues	314
Excluded volume	44587 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6rlw__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6rlw__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`6rlw__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`6rlw__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`6rlw__assembly_5__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	N-glycosylase/DNA lyase
Molecular weight formula_weight	37921.9 kDa
EC 编号 ec_number	3.2.2.-,4.2.99.18
Source method src_method	man
Copy count entity_count	5

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	AAA,BBB,CCC,DDD,EEE
Atom count atom_count	13184

MGSSHHHHHHSSGLVPRGSHMGHRTLASTPALWASIPCPRSELRLDLVLPSGQSFRWREQSPAHWSGVLADQVWTLTQTEEQLHCTVYRGDKSQASRPTPDELEAVRKYFQLDVTLAQLYHHWGSVDSHFQEVAQKFQGVRLLRQDPIECLFSFICSSNNNIARITGMVERLCQAFGPRLIQLDDVTYHGFPSLQALAGPEVEAHLRKLGLGYRARYVSASARAILEEQGGLAWLQQLRESSYEEAHKALCILPGVGTKVADCICLMALDKPQAVPVDVHMWHIAQRDYSWHPTTSQAKGPSPQTNKELGNFFRSLWGPYAGWAQAVLFSADLRQSR

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	4-(4-bromanyl-2-oxidanylidene-3~{H}-benzimidazol-1-yl)-~{N}-(4-iodophenyl)piperidine-1-carboxamide
Molecular weight formula_weight	541.2 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	771

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Unit-cell length a length_a	86.367 Å
Unit-cell length b length_b	86.367 Å
Unit-cell length c length_c	432.400 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	40

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	84.837 Å
R factor r_factor	—
R_work r_work	0.2225
R_free r_free	0.2741

Structure of the human 8-oxoguanine DNA Glycosylase hOGG1 in complex with inhibitor TH5487

1. Protein Identity and Related Structures Protein Identity & Related Structures

N-glycosylase/DNA lyase

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6rlw__assembly_1__model_1

6rlw__assembly_1__model_1 | I(q)

6rlw__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

7. Citations (1)

Structure of the human 8-oxoguanine DNA Glycosylase hOGG1 in complex with inhibitor TH5487

1. Protein Identity and Related Structures Protein Identity & Related Structures

N-glycosylase/DNA lyase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6rlw__assembly_1__model_1

6rlw__assembly_1__model_1 | I(q)

6rlw__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

7. Citations (1)