SAXSdb — 5l2x

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

DNA-directed primase/polymerase protein

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 2 PDB declaration: trimeric（3） Consistent with all polymer counts	Chain A； UniProt 1–353	Not recorded	;DNA (5'-D(PTPCPGPCP(5IU)PAPCPC)-3') ; × 1 ;DNA (5'-D(PGPGPTPAPGPCP(DDG))-3') ; × 1 DTP* 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；17-23% PEG 3350	Resolution 2.20 Å R-free 0.255
2	Protein–DNA Monomer Protein × 1 DNA 2 PDB declaration: trimeric（3） Consistent with all polymer counts	Chain B； UniProt 1–353	Not recorded	;DNA (5'-D(PTPCPGPCP(5IU)PAPCPC)-3') ; × 1 ;DNA (5'-D(PGPGPTPAPGPCP(DDG))-3') ; × 1 DTP* 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；17-23% PEG 3350	Resolution 2.20 Å R-free 0.255

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 5L2X	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5N85 Structure of RPA70N in complex with PrimPol (fragment 514-525) Deposited 2017-02-23	Different construct 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 514–528（15 aa） Fragment：UNP Residues 514-528	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；293.15 K；0.2 M Ammonium acetate 0.1 M Sodium acetate 4.5 20 % w/v PEG 3350	Resolution 2.00 Å R-free 0.228
5N8A Structure of RPA70N in complex with PrimPol (fragment 480-560) Deposited 2017-02-23	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain X 480–560（81 aa） Fragment：UNP residues 479-559	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293.15 K；0.2M imidazole malate, 30% w/v PEG 4000	Resolution 1.28 Å R-free 0.178
7JK1 Human PrimPol inserting correct dCTP opposite the 8-oxoguanine lesion Deposited 2020-07-27	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 1–354（354 aa）	Not recorded	DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 1 GOL GLYCEROL × 2 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；225-250 mM CaCl2 16-19% PEG 3350	Resolution 2.62 Å R-free 0.286
7JK1 Human PrimPol inserting correct dCTP opposite the 8-oxoguanine lesion Deposited 2020-07-27	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain B 1–354（354 aa）	Not recorded	DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；225-250 mM CaCl2 16-19% PEG 3350	Resolution 2.62 Å R-free 0.286
7JKL Human PrimPol misinserting dATP opposite the 8-oxoguanine lesion (3'-end base of the primer strand is 2',3'-dideoxy-terminated). Deposited 2020-07-28	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 1–354（354 aa）	Not recorded	DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；225- 250 mM CaCl2, 16 -19% PEG 3350	Resolution 2.38 Å R-free 0.277
7JKL Human PrimPol misinserting dATP opposite the 8-oxoguanine lesion (3'-end base of the primer strand is 2',3'-dideoxy-terminated). Deposited 2020-07-28	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain B 1–354（354 aa）	Not recorded	DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 2 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；225- 250 mM CaCl2, 16 -19% PEG 3350	Resolution 2.38 Å R-free 0.277
7JKP Human PrimPol misinserting dATP opposite the 8-oxoguanine lesion Deposited 2020-07-28	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 1–354（354 aa）	Not recorded	DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；225- 250 mM CaCl2 16 -19% PEG 3350	Resolution 2.59 Å R-free 0.307
7JKP Human PrimPol misinserting dATP opposite the 8-oxoguanine lesion Deposited 2020-07-28	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain B 1–354（354 aa）	Not recorded	DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；225- 250 mM CaCl2 16 -19% PEG 3350	Resolution 2.59 Å R-free 0.307
7JL8 Human PrimPol extending from the correct primer base C opposite the 8-oxoguanine lesion Deposited 2020-07-29	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 1–354（354 aa）	Not recorded	DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 1 GOL GLYCEROL × 2 EDO 1,2-ETHANEDIOL × 1 PEG DI(HYDROXYETHYL)ETHER × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；225-250 mM CaCl2, 16-19% PEG 3350	Resolution 2.10 Å R-free 0.213
7JL8 Human PrimPol extending from the correct primer base C opposite the 8-oxoguanine lesion Deposited 2020-07-29	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain B 1–354（354 aa）	Not recorded	DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 2 GOL GLYCEROL × 3 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；225-250 mM CaCl2, 16-19% PEG 3350	Resolution 2.10 Å R-free 0.213
7JLG Human PrimPol extending from the erroneous primer base A opposite the 8-oxoguanine lesion Deposited 2020-07-29	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 1–354（354 aa）	Not recorded	DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；225-250 mM CaCl2, 16-19% PEG 3350	Resolution 2.07 Å R-free 0.219
7JLG Human PrimPol extending from the erroneous primer base A opposite the 8-oxoguanine lesion Deposited 2020-07-29	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain B 1–354（354 aa）	Not recorded	DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 2 PEG DI(HYDROXYETHYL)ETHER × 1 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；225-250 mM CaCl2, 16-19% PEG 3350	Resolution 2.07 Å R-free 0.219

7 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PRIPO_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–353； UniProt 1–353 Author chain B； PDBConstruct 1–353； UniProt 1–353

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	5l2x
Deposition date deposition_date	2016-08-02
Structure title title	Crystal structure of human PrimPol ternary complex
Keywords keywords	Protein-DNA complex, TRANSFERASE-DNA complex; TRANSFERASE/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	29.68 Å
Radius of gyration Rg (electron density) rg_electron	28.31 Å
Forward intensity I(0) i0	97082000.00
Molecular weight molecular_weight	70436.0 kDa
Excluded volume excluded_volume	84933 Å³
Envelope volume envelope_volume	113540 Å³
Hydration-shell volume shell_volume	33403 Å³
Envelope diameter envelope_diameter	89.7 Å
Shell Rg shell_rg	35.77 Å
Envelope Rg envelope_rg	27.95 Å
Shape Rg shape_rg	28.26 Å
Total Rg total_rg	29.14 Å
Total atoms total_atoms	4903
Residues n_residues	552
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	92.0 Å
Rg (real space) rg_real	29.62 Å
Rg uncertainty (real space) rg_real_error	0.57 Å
I(0) (real space) i0_real	9.7080e+07
I(0) uncertainty (real space) i0_real_error	1.3530e+06
Rg (reciprocal space) rg_reciprocal	29.65 Å
I(0) (reciprocal space) i0_reciprocal	97080000.0000
Solution quality estimate total_estimate	0.9099
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	29.5 Å
Skewness Skewness skewness	0.177
Kurtosis Kurtosis kurtosis	-0.730
Angular range angular_range	— – 0.2650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	12520000.0000
Real-space data points n_real_points	54
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.959; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.954

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	DNA-directed primase/polymerase protein
Molecular weight formula_weight	40909.3 kDa
EC 编号 ec_number	2.7.7.-
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	5001

MNRKWEAKLKQIEERASHYERKPLSSVYRPRLSKPEEPPSIWRLFHRQAQAFNFVKSCKEDVHVFALECKVGDGQRIYLVTTYAEFWFYYKSRKNLLHCYEVIPENAVCKLYFDLEFNKPANPGADGKKMVALLIEYVCKALQELYGVNCSAEDVLNLDSSTDEKFSRHLIFQLHDVAFKDNIHVGNFLRKILQPALDLLGSEDDDSAPETTGHGFPHFSEAPARQGFSFNKMFTEKATEESWTSNSKKLERLGSAEQSSPDLSFLVVKNNMGEKHLFVDLGVYTRNRNFRLYKSSKIGKRVALEVTEDNKFFPIQSKDVSDEYQYFLSSLVSNVRFSDTLRILTCEPSQNKQ

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	Saccharomyces cerevisiae

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(PTPCPGPCP(5IU)PAPCPC)-3') ;
Molecular weight formula_weight	5149.1 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C,G

CATCGCUACCACACCCC

Entity 3 Entity 3 polymer

Description description	;DNA (5'-D(PGPGPTPAPGPCP*(DDG))-3') ;
Molecular weight formula_weight	4087.7 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	D,H

GGGTGTGGTAGCG

Entity 4 Entity 4 non-polymer

Description description	;2'-DEOXYADENOSINE 5'-TRIPHOSPHATE ;
Molecular weight formula_weight	491.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	98

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8. Citations (1)

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Unit-cell length a length_a	50.723 Å
Unit-cell length b length_b	65.212 Å
Unit-cell length c length_c	72.463 Å
Unit-cell angle α angle_alpha	67.89 °
Unit-cell angle β angle_beta	85.22 °
Unit-cell angle γ angle_gamma	86.65 °
Molecules per unit cell Z z_pdb	2

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

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	39.354 Å
R factor r_factor	0.2079
R_work r_work	0.2056
R_free r_free	0.2550

fit	/app/data/saxs_computation/l2/5l2x/5l2x.fit
pddf	/app/data/pr_computation/l2/5l2x/5l2x.pr.out
profile	/app/data/saxs_computation/l2/5l2x/5l2x.dat

Crystal structure of human PrimPol ternary complex

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

DNA-directed primase/polymerase protein

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 (6)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)