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6vbh

Human XPG endonuclease catalytic domain

Method: X-RAY DIFFRACTION Dmax: 85.8 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

DNA repair protein complementing XP-G cells,Flap endonuclease 1

Homo sapiens

UniProt O93634

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 89–128 Not recorded SO4 SULFATE ION × 15 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；288 K；Mixed 1:1 with 40% AmSO4, 200 mM Imidizole/Malate Buffer pH 4.2,100 mM MgCl2 X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；288 K；Mixed 1:1 wit 24% AmSO4, 200 mM Imidizole/Malate Buffer pH 4.2, 250 mM MgCl2, 0.5 mM SmSO4, 10 mM DTT X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；288 K；Mixed 1:1 with 32% AmSO4, 10 mM DTT, 200 mM Imidizole/Malate Buffer pH 4.2, and 50 mM MgCl2 Resolution 2.00 Å R-free 0.244
2 Insufficient information Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 89–128 Not recorded SO4 SULFATE ION × 30 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；288 K；Mixed 1:1 with 40% AmSO4, 200 mM Imidizole/Malate Buffer pH 4.2,100 mM MgCl2 X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；288 K；Mixed 1:1 wit 24% AmSO4, 200 mM Imidizole/Malate Buffer pH 4.2, 250 mM MgCl2, 0.5 mM SmSO4, 10 mM DTT X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；288 K；Mixed 1:1 with 32% AmSO4, 10 mM DTT, 200 mM Imidizole/Malate Buffer pH 4.2, and 50 mM MgCl2 Resolution 2.00 Å R-free 0.244

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 6VBH Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1B43 FEN-1 FROM P. FURIOSUS Deposited 1999-01-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–340（340 aa）
Chain B 1–340（340 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；60 % AMMONIUM SULFATE 100 MM IMIDAZOLE MALATE 50 MM MGCL2, pH 6.5
Resolution 2.00 Å R-free 0.279

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name FEN_PYRFU
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 85–124； UniProt 89–128

DNA repair protein complementing XP-G cells,Flap endonuclease 1

Homo sapiens

UniProt P28715

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 2–85 Chain A； UniProt 766–987 Not recorded SO4 SULFATE ION × 15 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；288 K；Mixed 1:1 with 40% AmSO4, 200 mM Imidizole/Malate Buffer pH 4.2,100 mM MgCl2 X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；288 K；Mixed 1:1 wit 24% AmSO4, 200 mM Imidizole/Malate Buffer pH 4.2, 250 mM MgCl2, 0.5 mM SmSO4, 10 mM DTT X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；288 K；Mixed 1:1 with 32% AmSO4, 10 mM DTT, 200 mM Imidizole/Malate Buffer pH 4.2, and 50 mM MgCl2 Resolution 2.00 Å R-free 0.244
2 Insufficient information Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 2–85 Chain A； UniProt 766–987 Not recorded SO4 SULFATE ION × 30 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；288 K；Mixed 1:1 with 40% AmSO4, 200 mM Imidizole/Malate Buffer pH 4.2,100 mM MgCl2 X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；288 K；Mixed 1:1 wit 24% AmSO4, 200 mM Imidizole/Malate Buffer pH 4.2, 250 mM MgCl2, 0.5 mM SmSO4, 10 mM DTT X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；288 K；Mixed 1:1 with 32% AmSO4, 10 mM DTT, 200 mM Imidizole/Malate Buffer pH 4.2, and 50 mM MgCl2 Resolution 2.00 Å R-free 0.244

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 6VBH Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5EKF Crystallization and X-ray Diffraction Data Collection of Importin-alpha from Mus musculus Complexed with a XPG NLS Peptide, fragment 1 Deposited 2015-11-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1054–1077（24 aa） Fragment：UNP residues 1054-1077
Chain C 1054–1077（24 aa） Fragment：UNP residues 1054-1077
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.6-0.7 M sodium citrate, 10 mM DTT
Resolution 2.00 Å R-free 0.192
6TUR human XPG, Apo1 form Deposited 2020-01-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain AAA 2–112（111 aa）
Chain AAA 750–990（241 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；25% PEG 3350, 100 mM Citric acid pH 3.5
Resolution 2.90 Å R-free 0.281
6TUR human XPG, Apo1 form Deposited 2020-01-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain BBB 2–112（111 aa）
Chain BBB 750–990（241 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；25% PEG 3350, 100 mM Citric acid pH 3.5
Resolution 2.90 Å R-free 0.281
6TUR human XPG, Apo1 form Deposited 2020-01-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain CCC 2–112（111 aa）
Chain CCC 750–990（241 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；25% PEG 3350, 100 mM Citric acid pH 3.5
Resolution 2.90 Å R-free 0.281
6TUR human XPG, Apo1 form Deposited 2020-01-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain DDD 2–112（111 aa）
Chain DDD 750–990（241 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；25% PEG 3350, 100 mM Citric acid pH 3.5
Resolution 2.90 Å R-free 0.281
6TUS human XPG, Apo2 form Deposited 2020-01-08 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–112（112 aa）
Chain A 750–990（241 aa）
Not recorded SO4 SULFATE ION × 3 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；25% PEG 3350, 100 mM Bis-Tris pH 6.5, 200 mM Amm. Sulfate.
Resolution 2.50 Å R-free 0.237
6TUS human XPG, Apo2 form Deposited 2020-01-08 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–112（112 aa）
Chain B 750–990（241 aa）
Not recorded SO4 SULFATE ION × 2 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；25% PEG 3350, 100 mM Bis-Tris pH 6.5, 200 mM Amm. Sulfate.
Resolution 2.50 Å R-free 0.237
6TUW human XPG-DNA, Complex 1 Deposited 2020-01-08 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–112（112 aa）
Chain A 750–990（241 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；5% PEG 3350, 50 mM Na Citrate pH 4.0
Resolution 3.50 Å R-free 0.293
6TUX human XPG-DNA, Complex 2 Deposited 2020-01-08 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–112（112 aa）
Chain A 750–986（237 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；5% PEG 3350, 50 mM Na Citrate pH 4.0
Resolution 3.10 Å R-free 0.303
6TUX human XPG-DNA, Complex 2 Deposited 2020-01-08 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain B 1–112（112 aa）
Chain B 750–986（237 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；5% PEG 3350, 50 mM Na Citrate pH 4.0
Resolution 3.10 Å R-free 0.303
9PD3 NER dual incision complex - DuIS Deposited 2025-06-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: 17-meric
Chain S 1–1186（1186 aa）
Mutation：D812N SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9PD4 NER dual incision complex - DuIM Deposited 2025-06-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric
Chain S 1–1186（1186 aa）
Mutation：D812N SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
9PD5 NER dual incision complex - NoF Deposited 2025-06-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain S 1–1186（1186 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.70 Å

8 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ERCC5_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–84； UniProt 2–85 Author chain A； PDBConstruct 125–346； UniProt 766–987

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.

SAXS scattering curve SAXS Profile

SAXS profile for 6vbh

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6vbh
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6vbh
Deposition date deposition_date2019-12-18
Structure title titleHuman XPG endonuclease catalytic domain
Keywords keywords;METALLOPROTEIN, REPLICATION, DNA DAMAGE, DNA REPAIR, NUCLOETIDE EXCISION REPAIR, XPG, Xeroderma pigmentosum, 5' NUCLEASE, HYDROLASE-DNA complex, DNA BINDING PROTEIN ;; DNA BINDING PROTEIN
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier24.12 Å
Radius of gyration Rg (electron density) rg_electron23.06 Å
Forward intensity I(0) i027861500.00
Molecular weight molecular_weight39227.0 kDa
Excluded volume excluded_volume48584 ų
Envelope volume envelope_volume61158 ų
Hydration-shell volume shell_volume22854 ų
Envelope diameter envelope_diameter88.7 Å
Shell Rg shell_rg29.39 Å
Envelope Rg envelope_rg23.35 Å
Shape Rg shape_rg23.03 Å
Total Rg total_rg23.96 Å
Total atoms total_atoms5400
Residues n_residues326
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax85.8 Å
Rg (real space) rg_real24.16 Å
Rg uncertainty (real space) rg_real_error0.67 Å
I(0) (real space) i0_real2.7860e+07
I(0) uncertainty (real space) i0_real_error3.7900e+05
Rg (reciprocal space) rg_reciprocal24.15 Å
I(0) (reciprocal space) i0_reciprocal27860000.0000
Solution quality estimate total_estimate0.7791
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary25.5 Å
Skewness Skewness skewness0.419
Kurtosis Kurtosis kurtosis-0.182
Angular range angular_range— – 0.3300 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha5529000.0000
Real-space data points n_real_points65
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.743; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.894; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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8. Citations (1)

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9. Files and Curves (10)