SAXSdb — 5um9

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

Flap endonuclease 1

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein–DNA Monomer Protein × 1 DNA 3 PDB declaration: tetrameric（4） Consistent with all polymer counts	Chain A； UniProt 2–336	Mutation：D86N	;DNA (5'-D(APCPTPCPTPGPCPCPTPCPAPAPGPAPCPGPGPT)-3') ; × 1 ;DNA (5'-D(PTPCPTPTPGPAPGPGPCPAPGPAPGPT)-3') ; × 1 ;DNA (5'-D(APCPCPGPTPCP*C)-3') ; × 1 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

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 5UM9	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1U7B Crystal structure of hPCNA bound to residues 331-350 of the flap endonuclease-1 (FEN1) Deposited 2004-08-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	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	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	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	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric	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	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric	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	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric	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	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric	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	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	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	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 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	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 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	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: pentameric	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	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric	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
5ZOD Crystal Structure of hFen1 in apo form Deposited 2018-04-13	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 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	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric	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	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric	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	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric	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	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 × 8 PDB declaration: decameric	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	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 × 5 PDB declaration: octameric	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	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 × 4 PDB declaration: octameric	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	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 × 4 PDB declaration: octameric	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	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 × 4 PDB declaration: octameric	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	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 × 4 PDB declaration: octameric	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	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 × 4 PDB declaration: octameric	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	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 × 4 PDB declaration: octameric	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	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 × 4 PDB declaration: octameric	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	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 × 4 PDB declaration: octameric	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	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 × 7 PDB declaration: decameric	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	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 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	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 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	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 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	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 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

26 other PDB entries and 30 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	FEN1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–335； UniProt 2–336

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	5um9
Deposition date deposition_date	2017-01-26
Structure title title	Flap endonuclease 1 (FEN1) D86N with 5'-flap substrate DNA and Sm3+
Keywords keywords	;dna repair, endonuclease, 5' nuclease, DNA binding, Hydrolase-DNA complex ;; Hydrolase/DNA
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	24.47 Å
Radius of gyration Rg (electron density) rg_electron	23.38 Å
Forward intensity I(0) i0	59335100.00
Molecular weight molecular_weight	51143.0 kDa
Excluded volume excluded_volume	60090 Å³
Envelope volume envelope_volume	77309 Å³
Hydration-shell volume shell_volume	27485 Å³
Envelope diameter envelope_diameter	81.8 Å
Shell Rg shell_rg	30.59 Å
Envelope Rg envelope_rg	23.58 Å
Shape Rg shape_rg	23.33 Å
Total Rg total_rg	24.25 Å
Total atoms total_atoms	6666
Residues n_residues	380
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	78.0 Å
Rg (real space) rg_real	24.42 Å
Rg uncertainty (real space) rg_real_error	0.43 Å
I(0) (real space) i0_real	5.9340e+07
I(0) uncertainty (real space) i0_real_error	7.6350e+05
Rg (reciprocal space) rg_reciprocal	24.43 Å
I(0) (reciprocal space) i0_reciprocal	59340000.0000
Solution quality estimate total_estimate	0.8966
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	29.7 Å
Skewness Skewness skewness	0.328
Kurtosis Kurtosis kurtosis	-0.297
Angular range angular_range	— – 0.3250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7471000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.887; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.991

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	Flap endonuclease 1
Molecular weight formula_weight	38510.2 kDa
EC 编号 ec_number	3.1.-.-
Mutation mutation	D86N
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	6701

GIQGLAKLIADVAPSAIRENDIKSYFGRKVAIDASMSIYQFLIAVRQGGDVLQNEEGETTSHLMGMFYRTIRMMENGIKPVYVFNGKPPQLKSGELAKRSERRAEAEKQLQQAQAAGAEQEVEKFTKRLVKVTKQHNDECKHLLSLMGIPYLDAPSEAEASCAALVKAGKVYAAATEDMDCLTFGSPVLMRHLTASEAKKLPIQEFHLSRILQELGLNQEQFVDLCILLGSDYCESIRGIGPKRAVDLIQKHKSIEEIVRRLDPNKYPVPENWLHKEAHQLFLEPEVLDPESVELKWSEPNEEELIKFMCGEKQFSEERIRSGVKRLSKSRQGSTLEVLFQ

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(APCPTPCPTPGPCPCPTPCPAPAPGPAPCPGPGPT)-3') ;
Molecular weight formula_weight	5476.6 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	D

ACTCTGCCTCAAGACGGT

Entity 3 Entity 3 polymer

Description description	;DNA (5'-D(PTPCPTPTPGPAPGPGPCPAPGPAPGPT)-3') ;
Molecular weight formula_weight	5266.4 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	E

ATATCTTGAGGCAGAGT

Entity 4 Entity 4 polymer

Description description	;DNA (5'-D(APCPCPGPTPCP*C)-3') ;
Molecular weight formula_weight	2058.4 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	F

ACCGTCC

Entity 5 Entity 5 non-polymer

Description description	POTASSIUM ION
Molecular weight formula_weight	39.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	SAMARIUM (III) ION
Molecular weight formula_weight	150.4 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	35

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	5um9A01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1010 — 5'-nuclease

Domain ID domain_id	5um9A02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	20 — 5' to 3' exonuclease, C-terminal subdomain

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8. Citations (1)

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Unit-cell length a length_a	105.846 Å
Unit-cell length b length_b	105.846 Å
Unit-cell length c length_c	100.709 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	2.805 Å
Low-resolution limit resolution_low	19.672 Å
R factor r_factor	0.2107
R_work r_work	0.2078
R_free r_free	0.2659

fit	/app/data/saxs_computation/um/5um9/5um9.fit
pddf	/app/data/pr_computation/um/5um9/5um9.pr.out
profile	/app/data/saxs_computation/um/5um9/5um9.dat

Flap endonuclease 1 (FEN1) D86N with 5'-flap substrate DNA and Sm3+

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

Flap endonuclease 1

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)