SAXSdb — 7ozt

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

Cyclin-dependent kinase inhibitor 2A

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain BBB； UniProt 1–156	Not recorded	Camelid nanobody NB09 × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；291 K；Molecular Dimensions Morpheus screen condition G4	Resolution 1.74 Å R-free 0.209

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 7OZT	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1A5E SOLUTION NMR STRUCTURE OF TUMOR SUPPRESSOR P16INK4A, 18 STRUCTURES Deposited 1998-02-13	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 1–156（156 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.5；293 K；Ionic strength (raw mmCIF value) CA. 0；Pressure NO NMR sample composition H2O AND D2O	Resolution not provided
1BI7 MECHANISM OF G1 CYCLIN DEPENDENT KINASE INHIBITION FROM THE STRUCTURE OF THE CDK6-P16INK4A TUMOR SUPPRESSOR COMPLEX Deposited 1998-06-22	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–156（156 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.40 Å R-free 0.330
1DC2 SOLUTION NMR STRUCTURE OF TUMOR SUPPRESSOR P16INK4A, 20 STRUCTURES Deposited 1999-11-04	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 1–156（156 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.5；293 K；Ionic strength (raw mmCIF value) 0；Pressure AMBIENT NMR sample composition 0.2-0.4 MM P16INK4A U-15N,13C; 4 MM HEPES, 1 MM DTT, 5 UM EDTA; 95% H2O, 5% D2O NMR sample composition 0.2-0.4 MM P16INK4A U-15N; 4 MM HEPES, 1 MM DTT, 5 UM EDTA; 95% H2O, 5% D2O NMR sample composition 0.2-0.4 MM P16INK4A; 4 MM HEPES, 1 MM DTT, 5 UM EDTA; 95% H2O, 5% D2O	Resolution not provided
2A5E SOLUTION NMR STRUCTURE OF TUMOR SUPPRESSOR P16INK4A, RESTRAINED MINIMIZED MEAN STRUCTURE Deposited 1998-02-13	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 1–156（156 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.5；293 K；Ionic strength (raw mmCIF value) CA. 0；Pressure NO NMR sample composition H2O AND D2O	Resolution not provided

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CDN2A_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain BBB； PDBConstruct 20–175； UniProt 1–156

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	7ozt
Deposition date deposition_date	2021-06-28
Structure title title	Nanobodies restore stability to cancer-associated mutants of tumor suppressor protein p16INK4a
Keywords keywords	nanobody-p16INK4A complex, tumour-suppressor, Checkpoint, pharmacological chaperone, CELL CYCLE; CELL CYCLE
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	20.08 Å
Radius of gyration Rg (electron density) rg_electron	19.29 Å
Forward intensity I(0) i0	13448900.00
Molecular weight molecular_weight	26406.0 kDa
Excluded volume excluded_volume	32612 Å³
Envelope volume envelope_volume	38471 Å³
Hydration-shell volume shell_volume	17236 Å³
Envelope diameter envelope_diameter	68.4 Å
Shell Rg shell_rg	25.03 Å
Envelope Rg envelope_rg	19.56 Å
Shape Rg shape_rg	19.29 Å
Total Rg total_rg	20.09 Å
Total atoms total_atoms	3692
Residues n_residues	247
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	67.8 Å
Rg (real space) rg_real	20.07 Å
Rg uncertainty (real space) rg_real_error	0.52 Å
I(0) (real space) i0_real	1.3450e+07
I(0) uncertainty (real space) i0_real_error	1.9180e+05
Rg (reciprocal space) rg_reciprocal	20.07 Å
I(0) (reciprocal space) i0_reciprocal	13450000.0000
Solution quality estimate total_estimate	0.7111
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.3 Å
Skewness Skewness skewness	0.319
Kurtosis Kurtosis kurtosis	-0.421
Angular range angular_range	— – 0.3950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4092000.0000
Real-space data points n_real_points	71
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.846; Stabil: 1.000; Sysdev: 0.260; Positv: 1.000; Valcen: 0.975; Smooth: 0.946

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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	Camelid nanobody NB09
Molecular weight formula_weight	14208.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	AAA
Atom count atom_count	3830

QVQLVESGGGLVQAGASLRLSCAASGSTYMFSISAMGWYRQAPGKQRELVAAITSGGGDTNYADSVKGRFTISRDRAKNMVYLQMNSLKPEDTAVYYCNFAPGLQSVRSGSWGQGTQVTVSSHHHHHHEPEA

来源 Source

来源生物 organism	Lama glama
通用名 common_name	Llama
NCBI Class编号 ncbi_taxonomy_id	9844
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Cyclin-dependent kinase inhibitor 2A
Molecular weight formula_weight	18701.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	BBB

MAHHHHHHSSGLEVLFQGPMEPAAGSSMEPSADWLATAAARGRVEEVRALLEAGALPNAPNSYGRRPIQVMMMGSARVAELLLLHGAEPNCADPATLTRPVHDAAREGFLDTLVVLHRAGARLDVRDAWGRLPVDLAEELGHRDVARYLRAAAGGTRGSNHARIDAAEGPSDIPD

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 BL21(DE3)

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	90

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8. Citations (1)

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Unit-cell length a length_a	42.119 Å
Unit-cell length b length_b	182.931 Å
Unit-cell length c length_c	65.225 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	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	1.740 Å
Low-resolution limit resolution_low	91.465 Å
R factor r_factor	—
R_work r_work	0.1798
R_free r_free	0.2086

fit	/app/data/saxs_computation/oz/7ozt/7ozt.fit
pddf	/app/data/pr_computation/oz/7ozt/7ozt.pr.out
profile	/app/data/saxs_computation/oz/7ozt/7ozt.dat

Nanobodies restore stability to cancer-associated mutants of tumor suppressor protein p16INK4a

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

Cyclin-dependent kinase inhibitor 2A

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

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)