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Protein Structures and Oligomeric States

Enter a protein name, UniProt accession or PDB ID. Name searches ask you to confirm the protein identity before related structures are queried.

Current Protein Identity：P39748 New Search
27PDB entries
31Biological assembly
33chain/assembly records
Main Difference Dimensions in This Set
Different construct Different mutation/modification Different assembly state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics

Difference tags compare only the current result set; every original PDB and assembly record remains separate.

Related-Structure Differences

Each row represents one biological assembly in one PDB entry; multiple monomers of the same protein are listed separately.

PDB Entry Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Experimental Method Experimental Conditions Structure Quality
1U7B Crystal structure of hPCNA bound to residues 331-350 of the flap endonuclease-1 (FEN1) Deposited 2004-08-03 Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count
Chain B 331–350（20 aa） Fragment：PIP-box region of FEN-1 (residues 331-350)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；ammonium sulfate, sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.88 Å R-free 0.265
1UL1 Crystal structure of the human FEN1-PCNA complex Deposited 2003-09-05 Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count
Chain X 2–380（379 aa）
Chain Y 2–380（379 aa）
Chain Z 2–380（379 aa）
Not recorded MG MAGNESIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；283 K；6% PEG1000, 50mM MES, 50mM Sodium chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 283K
Resolution 2.90 Å R-free 0.284
3Q8K Crystal Structure of Human Flap Endonuclease FEN1 (WT) in complex with product 5'-flap DNA, SM3+, and K+ Deposited 2011-01-06 Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric（4） Consistent with all polymers
Chain A 2–336（335 aa）
Not recorded SM SAMARIUM (III) ION × 4 K POTASSIUM ION × 1 OH HYDROXIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；288 K；16% mPEG 2k, 20% saturated KCl, 0.5 mM Sm2(SO4)3, 10 mM Mg(NO3)2, 100 mM Hepes pH 7.0, 5% ethylene glycol, VAPOR DIFFUSION, temperature 288K
Resolution 2.20 Å R-free 0.213
3Q8L Crystal Structure of Human Flap Endonuclease FEN1 (WT) in complex with substrate 5'-flap DNA, SM3+, and K+ Deposited 2011-01-06 Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric（4） Consistent with all polymers
Chain A 2–336（335 aa）
Not recorded SM SAMARIUM (III) ION × 4 K POTASSIUM ION × 1 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；288 K；17% mPEG 2k, 20% KCl, 0.5 mM Sm2(SO4)3, 50 mM Bis-Tris pH 7.0 and 5% Ethylene Glycol, vapor diffusion, temperature 288K
Resolution 2.32 Å R-free 0.202
3Q8M Crystal Structure of Human Flap Endonuclease FEN1 (D181A) in complex with substrate 5'-flap DNA and K+ Deposited 2011-01-06 Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric（4） Consistent with all polymers
Chain A 2–336（335 aa） Fragment：D181A
Not recorded K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；288 K；20% mPEG 2k, 20% KCl, 10 mM CaCl2, 50 mM Bis-Tris pH 7.5, 5% ethylene glycol, vapor diffusion, temperature 288K
Resolution 2.60 Å R-free 0.272
3Q8M Crystal Structure of Human Flap Endonuclease FEN1 (D181A) in complex with substrate 5'-flap DNA and K+ Deposited 2011-01-06 Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric（4） Consistent with all polymers
Chain B 2–336（335 aa） Fragment：D181A
Not recorded K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；288 K；20% mPEG 2k, 20% KCl, 10 mM CaCl2, 50 mM Bis-Tris pH 7.5, 5% ethylene glycol, vapor diffusion, temperature 288K
Resolution 2.60 Å R-free 0.272
3UVU Structural basis of nuclear import of Flap endonuclease 1 (FEN1) Deposited 2011-11-30 Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain B 352–370（19 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；293 K；Sodium citrate, DTT, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.38 Å R-free 0.215
5FV7 Human Fen1 in complex with an N-hydroxyurea compound Deposited 2016-02-03 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 1–336（336 aa） Fragment：RESIDUES 1-336
Not recorded MG MAGNESIUM ION × 2 R3Z 1-[(2S)-2,3-dihydro-1,4-benzodioxin-2-ylmethyl]-3-hydroxythieno[3,2-d]pyrimidine-2,4(1H,3H)-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；25% PEG3350, 0.1M MOPS 7.0, 5% 2-PROPANOL, 2% GLYCEROL, pH 7.5
Resolution 2.84 Å R-free 0.300
5FV7 Human Fen1 in complex with an N-hydroxyurea compound Deposited 2016-02-03 Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain B 1–336（336 aa） Fragment：RESIDUES 1-336
Not recorded MG MAGNESIUM ION × 2 R3Z 1-[(2S)-2,3-dihydro-1,4-benzodioxin-2-ylmethyl]-3-hydroxythieno[3,2-d]pyrimidine-2,4(1H,3H)-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；25% PEG3350, 0.1M MOPS 7.0, 5% 2-PROPANOL, 2% GLYCEROL, pH 7.5
Resolution 2.84 Å R-free 0.300
5K97 Flap endonuclease 1 (FEN1) D233N with cleaved product fragment and Sm3+ Deposited 2016-05-31 Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: pentameric（5） Consistent with all polymers
Chain A 2–336（335 aa）
Mutation：D233N SM SAMARIUM (III) ION × 8 K POTASSIUM ION × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；283 K；24% MPEG 2K, 20% KCl, 5% ethylene glycol, 100 mM HEPES pH 7.5
Resolution 2.10 Å R-free 0.219
5KSE Flap endonuclease 1 (FEN1) R100A with 5'-flap substrate DNA and Sm3+ Deposited 2016-07-08 Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric（4） Consistent with all polymers
Chain A 2–336（335 aa）
Mutation：R100A SM SAMARIUM (III) ION × 5 K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；288 K；22% mPEG 2000, 20% saturated KCl, 5% ethylene glycol, 100 mM HEPES pH 7.5
Resolution 2.10 Å R-free 0.245
5UM9 Flap endonuclease 1 (FEN1) D86N with 5'-flap substrate DNA and Sm3+ Deposited 2017-01-26 Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric（4） Consistent with all polymers
Chain A 2–336（335 aa）
Mutation：D86N K POTASSIUM ION × 1 SM SAMARIUM (III) ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；283 K；6% MPEG 2K, 10% KCl, 50 mM HEPES pH 7.5, 2.5% Ethylene glycol, 1.06 mM SmSO4
Resolution 2.81 Å R-free 0.266
5ZOD Crystal Structure of hFen1 in apo form Deposited 2018-04-13 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 1–333（333 aa） Fragment：nuclease core
Not recorded MG MAGNESIUM ION × 2 K POTASSIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.8；298 K；PEG 3350, MgCl2, Tris, KCl
Resolution 1.90 Å R-free 0.226
5ZOE Crystal Structure of D181A hFen1 in complex with DNA Deposited 2018-04-13 Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric（4） Consistent with all polymers
Chain A 1–333（333 aa） Fragment：nuclease core (1-333)
Mutation：D181A K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.8；298 K；PEG 3350, MgCl2, Tris, KCl
Resolution 1.95 Å R-free 0.227
5ZOF Crystal Structure of D181A/R192F hFen1 in complex with DNA Deposited 2018-04-13 Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric（4） Consistent with all polymers
Chain A 1–333（333 aa） Fragment：nuclease core (1-333)
Mutation：D181A, R192F K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.8；298 K；PEG 3350, MgCl2, Tris, KCl
Resolution 2.25 Å R-free 0.269
5ZOG Crystal Structure of R192F hFen1 in complex with DNA Deposited 2018-04-13 Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric（4） Consistent with all polymers
Chain A 1–333（333 aa） Fragment：nuclease core (1-333)
Mutation：R192F No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.8；298 K；PEG 3350, MgCl2, Tris, KCl
Resolution 2.30 Å R-free 0.231
6TNZ Human polymerase delta-FEN1-PCNA toolbelt Deposited 2019-12-10 Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers
Chain H 1–380（380 aa）
Not recorded ZN ZINC ION × 1 SF4 IRON/SULFUR CLUSTER × 1 TTP THYMIDINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.05 Å
7QO1 complex of DNA ligase I and FEN1 on PCNA and DNA Deposited 2021-12-23 Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: octameric（8） Consistent with all polymers
Chain Y 1–380（380 aa）
Mutation：D181A AMP ADENOSINE MONOPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
8YJH Structure of the human endogenous PCNA-FEN1 complex - State A Deposited 2024-03-01 Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: octameric（8） Consistent with all polymers
Chain D 1–380（380 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.68 Å
8YJL Structure of the human endogenous PCNA-FEN1 complex - State B Deposited 2024-03-02 Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: octameric（8） Consistent with all polymers
Chain D 1–380（380 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.51 Å
8YJQ Structure of the human endogenous PCNA-FEN1 complex - State C Deposited 2024-03-02 Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: octameric（8） Consistent with all polymers
Chain D 1–380（380 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.51 Å
8YJR Structure of the human endogenous PCNA-FEN1 complex - State D Deposited 2024-03-02 Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: octameric（8） Consistent with all polymers
Chain D 1–380（380 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.51 Å
8YJS Structure of the human endogenous PCNA-FEN1 complex - State E Deposited 2024-03-02 Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: octameric（8） Consistent with all polymers
Chain D 1–380（380 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.55 Å
8YJU Structure of the human endogenous PCNA-FEN1 complex - State F Deposited 2024-03-02 Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: octameric（8） Consistent with all polymers
Chain D 1–380（380 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.78 Å
8YJV Structure of the human endogenous PCNA-FEN1 complex - State G Deposited 2024-03-03 Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: octameric（8） Consistent with all polymers
Chain D 1–380（380 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.51 Å
8YJW Structure of the human endogenous PCNA-FEN1 complex - State H Deposited 2024-03-03 Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: octameric（8） Consistent with all polymers
Chain D 1–380（380 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.55 Å
8YJZ Structure of the human endogenous PCNA-FEN1-RNase H2 complex - State D Deposited 2024-03-03 Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: decameric（10） Consistent with all polymers
Chain D 1–380（380 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.15 Å
9RCI Crystal Structure of Flap Endonuclease FEN1 with Compound 28 Deposited 2025-05-29 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 1–336（336 aa）
Not recorded MG MAGNESIUM ION × 2 EDO 1,2-ETHANEDIOL × 1 A1JD4 (3~{S})-13-[(1~{S})-1-(2-methylquinolin-7-yl)ethoxy]-11-oxidanyl-5-oxa-1,8-diazatricyclo[8.4.0.0^{3,8}]tetradeca-10,13-diene-9,12-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；277 K；21 % PEG MME 5000, 0.1 M MES pH 6.5, 10 mM ammonium sulphate
Resolution 1.66 Å R-free 0.283
9RCI Crystal Structure of Flap Endonuclease FEN1 with Compound 28 Deposited 2025-05-29 Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain B 1–336（336 aa）
Not recorded MG MAGNESIUM ION × 2 EDO 1,2-ETHANEDIOL × 1 A1JD4 (3~{S})-13-[(1~{S})-1-(2-methylquinolin-7-yl)ethoxy]-11-oxidanyl-5-oxa-1,8-diazatricyclo[8.4.0.0^{3,8}]tetradeca-10,13-diene-9,12-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；277 K；21 % PEG MME 5000, 0.1 M MES pH 6.5, 10 mM ammonium sulphate
Resolution 1.66 Å R-free 0.283
9RDI Crystal Structure of Flap Endonuclease FEN1 with Compound 5 Deposited 2025-06-02 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 1–336（336 aa）
Not recorded A1JED 2-methyl-9-oxidanyl-6-(phenylmethyl)-3,4-dihydropyrazino[1,2-c]pyrimidine-1,8-dione × 1 TEW 6-tungstotellurate(VI) × 4 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；277 K；21 % PEG MME 5000, 0.1 M MES pH 6.5, 10 mM ammonium sulphate
Resolution 2.10 Å R-free 0.232
9RDI Crystal Structure of Flap Endonuclease FEN1 with Compound 5 Deposited 2025-06-02 Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain B 1–336（336 aa）
Not recorded A1JED 2-methyl-9-oxidanyl-6-(phenylmethyl)-3,4-dihydropyrazino[1,2-c]pyrimidine-1,8-dione × 1 TEW 6-tungstotellurate(VI) × 5 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；277 K；21 % PEG MME 5000, 0.1 M MES pH 6.5, 10 mM ammonium sulphate
Resolution 2.10 Å R-free 0.232

This page presents structural evidence recorded in PDB/mmCIF.“No recorded non-water small molecule” does not prove that the experimental sample was ligand-free; experimental conditions belong to the PDB experiment, while ligands and copy counts are shown for each biological assembly.