SAXSdb — 1zzj

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

Heterogeneous nuclear ribonucleoprotein K

Homo sapiens

UniProt P61978

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 Homooligomer Protein × 3 DNA 1 PDB declaration: tetrameric（4） Consistent with all polymer counts	Chain A； UniProt 385–463 Chain B； UniProt 385–463 Chain C； UniProt 385–463	Fragment：KH3 domain	5'-D(TPTPCPCPCPCPTPCPCPCPCPAPTPTP*T)-3' × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；PEG 8000, SODIUM ACETATE, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.30 Å R-free 0.283

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 1ZZJ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1J5K COMPLEX OF THE KH3 DOMAIN OF HNRNP K WITH A SINGLE_STRANDED 10MER DNA OLIGONUCLEOTIDE Deposited 2002-05-13	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 379–463（85 aa） Fragment：KH3 domain, RESIDUES 379-463, NUMBERED 5-89	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.8；308 K；Ionic strength (raw mmCIF value) 50 mM SODIUM PHOSPHATE	Resolution not provided
1KHM C-TERMINAL KH DOMAIN OF HNRNP K (KH3) Deposited 1999-01-07	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 375–463（89 aa） Fragment：C-TERMINAL KH DOMAIN, RESIDUES 379-463 OF FULL LENGTH HNRNP K	Mutation：G26R	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.5；300 K；Ionic strength (raw mmCIF value) 5 mM；Pressure 1	Resolution not provided
1ZZI Crystal Structure Analysis of the third KH domain of hnRNP K in complex with ssDNA Deposited 2005-06-14	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 385–463（79 aa） Fragment：KH3 domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；294 K；PEG 4000, TRIS HCl, MAGNESIUM CHLORIDE, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 1.80 Å R-free 0.240
1ZZI Crystal Structure Analysis of the third KH domain of hnRNP K in complex with ssDNA Deposited 2005-06-14	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: dimeric	Chain B 385–463（79 aa） Fragment：KH3 domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；294 K；PEG 4000, TRIS HCl, MAGNESIUM CHLORIDE, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 1.80 Å R-free 0.240
1ZZK Crystal Structure of the third KH domain of hnRNP K at 0.95A resolution Deposited 2005-06-14	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 385–463（79 aa） Fragment：KH3 domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；294 K；ammonium sulphate, PEG 400, Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 0.95 Å R-free 0.127
7CRU hnRNPK NLS in complex with Importin alpha 1 (KPNA2) Deposited 2020-08-14	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 18–38（21 aa）	Not recorded	ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；0.1 M Ammonium Acetate, 0.1 M Bis-Tris pH 5.5, 17% w/v PEG 10000	Resolution 2.80 Å R-free 0.240
7CRU hnRNPK NLS in complex with Importin alpha 1 (KPNA2) Deposited 2020-08-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 18–38（21 aa）	Not recorded	ACT ACETATE ION × 4 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；0.1 M Ammonium Acetate, 0.1 M Bis-Tris pH 5.5, 17% w/v PEG 10000	Resolution 2.80 Å R-free 0.240
7RJK Crystal structure of human Bromodomain containing protein 3 (BRD3) in complex with hnRNPK Deposited 2021-07-21	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 C 57–66（10 aa） Fragment：UNP residues 57-66	Non-standard monomer：Yes (specific site not provided by mmCIF)	EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；292 K；2.0 M ammonium sulfate, 0.1 M sodium citrate tribasic dihydrate, 0.2 M potassium/sodium tartrate tetrahydrate	Resolution 1.85 Å R-free 0.217
7RJK Crystal structure of human Bromodomain containing protein 3 (BRD3) in complex with hnRNPK Deposited 2021-07-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 57–66（10 aa） Fragment：UNP residues 57-66	Non-standard monomer：Yes (specific site not provided by mmCIF)	EDO 1,2-ETHANEDIOL × 1 SO4 SULFATE ION × 2 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；292 K；2.0 M ammonium sulfate, 0.1 M sodium citrate tribasic dihydrate, 0.2 M potassium/sodium tartrate tetrahydrate	Resolution 1.85 Å R-free 0.217
7RJO Crystal structure of human Bromodomain containing protein 4 (BRD4) in complex with hnRNPK Deposited 2021-07-21	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 57–66（10 aa） Fragment：UNP residues 57-66	Non-standard monomer：Yes (specific site not provided by mmCIF)	NA SODIUM ION × 1 GOL GLYCEROL × 2 ACT ACETATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；292 K；25% w/v PEG3350, 0.2 M ammonium acetate, 0.1 M Bis-Tris	Resolution 1.38 Å R-free 0.198

7 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	HNRPK_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 4–82； UniProt 385–463 Author chain B； PDBConstruct 4–82； UniProt 385–463 Author chain C； PDBConstruct 4–82； UniProt 385–463

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	1zzj
Deposition date deposition_date	2005-06-14
Structure title title	Structure of the third KH domain of hnRNP K in complex with 15-mer ssDNA
Keywords keywords	PROTEIN-DNA COMPLEX, STRUCTURAL PROTEIN-DNA COMPLEX; STRUCTURAL PROTEIN/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	22.61 Å
Radius of gyration Rg (electron density) rg_electron	22.39 Å
Forward intensity I(0) i0	13266700.00
Molecular weight molecular_weight	25433.0 kDa
Excluded volume excluded_volume	31111 Å³
Envelope volume envelope_volume	40452 Å³
Hydration-shell volume shell_volume	16377 Å³
Envelope diameter envelope_diameter	85.3 Å
Shell Rg shell_rg	26.99 Å
Envelope Rg envelope_rg	22.60 Å
Shape Rg shape_rg	22.41 Å
Total Rg total_rg	22.96 Å
Total atoms total_atoms	1775
Residues n_residues	230
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	82.5 Å
Rg (real space) rg_real	22.80 Å
Rg uncertainty (real space) rg_real_error	0.75 Å
I(0) (real space) i0_real	1.3270e+07
I(0) uncertainty (real space) i0_real_error	1.7620e+05
Rg (reciprocal space) rg_reciprocal	22.75 Å
I(0) (reciprocal space) i0_reciprocal	13270000.0000
Solution quality estimate total_estimate	0.6158
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.2 Å
Skewness Skewness skewness	0.535
Kurtosis Kurtosis kurtosis	-0.148
Angular range angular_range	— – 0.3500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2037000.0000
Real-space data points n_real_points	67
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.686; Stabil: 1.000; Sysdev: 0.130; Positv: 1.000; Valcen: 0.659; Smooth: 0.893

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	5'-D(TPTPCPCPCPCPTPCPCPCPCPAPTPTP*T)-3'
Molecular weight formula_weight	4406.9 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	D
Atom count atom_count	1855

TTCCCCTCCCCATTT

Entity 2 Entity 2 polymer

Description description	Heterogeneous nuclear ribonucleoprotein K
Molecular weight formula_weight	8910.1 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C

GAMGPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQNSVKQYSGKFF

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 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	80

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7. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1zzja2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.51 — Eukaryotic type KH-domain (KH-domain type I)
Superfamily Superfamily superfamily	d.51.1 — Eukaryotic type KH-domain (KH-domain type I)
Family Family family	d.51.1.0 — automated matches

Domain ID domain_id	d1zzja3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1zzjb2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.51 — Eukaryotic type KH-domain (KH-domain type I)
Superfamily Superfamily superfamily	d.51.1 — Eukaryotic type KH-domain (KH-domain type I)
Family Family family	d.51.1.0 — automated matches

Domain ID domain_id	d1zzjb3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1zzjc2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.51 — Eukaryotic type KH-domain (KH-domain type I)
Superfamily Superfamily superfamily	d.51.1 — Eukaryotic type KH-domain (KH-domain type I)
Family Family family	d.51.1.0 — automated matches

Domain ID domain_id	d1zzjc3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (3 domains)

Domain ID domain_id	1zzjA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1370 — Ribosomal Protein S8; Chain: A, domain 1
Homologous superfamily homologous superfamily	10 — K Homology domain, type 1

Domain ID domain_id	1zzjB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1370 — Ribosomal Protein S8; Chain: A, domain 1
Homologous superfamily homologous superfamily	10 — K Homology domain, type 1

Domain ID domain_id	1zzjC00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1370 — Ribosomal Protein S8; Chain: A, domain 1
Homologous superfamily homologous superfamily	10 — K Homology domain, type 1

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8. Citations (1)

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Unit-cell length a length_a	54.008 Å
Unit-cell length b length_b	54.008 Å
Unit-cell length c length_c	149.656 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	18

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

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2132
R_work r_work	0.2097
R_free r_free	0.2828

fit	/app/data/saxs_computation/zz/1zzj/1zzj.fit
pddf	/app/data/pr_computation/zz/1zzj/1zzj.pr.out
profile	/app/data/saxs_computation/zz/1zzj/1zzj.dat

Structure of the third KH domain of hnRNP K in complex with 15-mer ssDNA

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

Heterogeneous nuclear ribonucleoprotein K

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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (6 domains)

CATH v4.4 (3 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)