SAXSdb — 3dal

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

PR domain zinc finger protein 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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 2–187 Chain B； UniProt 2–187	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；Purified PRDM1 was crystallized using hanging drop vapor diffusion method at 20 C by mixing 1.5 l of the protein solution with 1.5 l of the reservoir solution containing 2.0 M Na Formide, 0.1 M sodium acetate, pH 4.6., VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.65 Å R-free 0.217

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 3DAL	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9Q1G Blimp-1 with compound 5 Deposited 2025-08-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric	Chain A 38–223（186 aa） Chain B 38–223（186 aa） Chain C 38–223（186 aa） Chain D 38–223（186 aa） Chain E 38–223（186 aa） Chain F 38–223（186 aa） Chain G 38–223（186 aa） Chain H 38–223（186 aa）	Mutation：37-222 Mutation：37-222 Mutation：37-222 Mutation：37-222 Mutation：37-222 Mutation：37-222 Mutation：37-222 Mutation：37-222	A1CNQ (2S)-2-(4-bromophenyl)-2-(5,8-dihydropyrido[3,4-d]pyrimidin-7(6H)-yl)acetamide × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；100mM Sodium Cacodylate pH 5.5, 15% w/v PEG 6k, 0.15M Potassium Thiocyanate	Resolution 3.70 Å R-free 0.253
9Q33 Cereblon Ternary Complex with Blimp1 and compound 5 Deposited 2025-08-15	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 38–223（186 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 3.20 Å

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PRDM1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 11–196； UniProt 2–187 Author chain B； PDBConstruct 11–196； UniProt 2–187

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	3dal
Deposition date deposition_date	2008-05-29
Structure title title	Methyltransferase domain of human PR domain-containing protein 1
Keywords keywords	;Methyltransferase, PRDM1, Structural Genomics, Structural Genomics Consortium, SGC, DNA-binding, Metal-binding, Nucleus, Polymorphism, Repressor, Transcription, Transcription regulation, Zinc, Zinc-finger, DNA BINDING PROTEIN, TRANSFERASE ;; TRANSFERASE
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	24.33 Å
Radius of gyration Rg (electron density) rg_electron	23.42 Å
Forward intensity I(0) i0	26691400.00
Molecular weight molecular_weight	39724.0 kDa
Excluded volume excluded_volume	49725 Å³
Envelope volume envelope_volume	62781 Å³
Hydration-shell volume shell_volume	22781 Å³
Envelope diameter envelope_diameter	86.9 Å
Shell Rg shell_rg	29.86 Å
Envelope Rg envelope_rg	23.96 Å
Shape Rg shape_rg	23.39 Å
Total Rg total_rg	24.34 Å
Total atoms total_atoms	2805
Residues n_residues	345
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	83.4 Å
Rg (real space) rg_real	24.34 Å
Rg uncertainty (real space) rg_real_error	0.65 Å
I(0) (real space) i0_real	2.6690e+07
I(0) uncertainty (real space) i0_real_error	3.9050e+05
Rg (reciprocal space) rg_reciprocal	24.34 Å
I(0) (reciprocal space) i0_reciprocal	26690000.0000
Solution quality estimate total_estimate	0.8755
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.2 Å
Skewness Skewness skewness	0.330
Kurtosis Kurtosis kurtosis	-0.428
Angular range angular_range	— – 0.3250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4862000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.823; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.910; Smooth: 0.999

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	3dalA00
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	270 — Beta-clip-like
Homologous superfamily homologous superfamily	10 — SET domain

Domain ID domain_id	3dalB00
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	270 — Beta-clip-like
Homologous superfamily homologous superfamily	10 — SET domain

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8. Citations (1)

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Unit-cell length a length_a	64.834 Å
Unit-cell length b length_b	64.960 Å
Unit-cell length c length_c	112.663 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	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.650 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.1970
R_work r_work	0.1960
R_free r_free	0.2170

Description description	PR domain zinc finger protein 1
Molecular weight formula_weight	22692.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3199

Methyltransferase domain of human PR domain-containing protein 1

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

PR domain zinc finger protein 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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 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)

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

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	307

fit	/app/data/saxs_computation/da/3dal/3dal.fit
pddf	/app/data/pr_computation/da/3dal/3dal.pr.out
profile	/app/data/saxs_computation/da/3dal/3dal.dat