SAXSdb — 1ud7

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

PROTEIN (UBIQUITIN CORE MUTANT 1D7)

OrganismNot specified

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 41–116	Mutation：I3V,V5L,I13V,L15I,I23V,V26F,I67L	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 5.8；303 K；Pressure 1	Resolution not provided

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 1UD7	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CMX STRUCTURAL BASIS FOR THE SPECIFICITY OF UBIQUITIN C-TERMINAL HYDROLASES Deposited 1999-05-12	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–75（75 aa） Fragment：ALL Chain D 1–75（75 aa） Fragment：ALL	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.5；16% PEG 6000 0.1 M SODIUM ACETATE PH 4.4, pH 4.5	Resolution 2.25 Å R-free 0.285
1GJZ Solution structure of a dimeric N-terminal fragment of human ubiquitin Deposited 2001-08-06	Different construct Different mutation/modification Different oligomeric state Different experimental conditions	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–51（51 aa） Fragment：RESIDUES 1-51 Chain B 1–51（51 aa） Fragment：RESIDUES 1-51	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 800MM SODIUM SULPHATE；Pressure 1	Resolution not provided
1UZX A complex of the Vps23 UEV with ubiquitin Deposited 2004-03-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–76（76 aa）	Not recorded	MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；22% PEG 8000, 0.1M MES PH 6.5, 0.2M (NH4)2SO4	Resolution 1.85 Å R-free 0.274

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	UBIQ_HUMANX
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–76； UniProt 41–116

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	1ud7
Deposition date deposition_date	1999-04-07
Structure title title	SOLUTION STRUCTURE OF THE DESIGNED HYDROPHOBIC CORE MUTANT OF UBIQUITIN, 1D7
Keywords keywords	UBIQUITIN, DESIGNED CORE MUTANT; UBIQUITIN
Experimental Method method	SOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier	12.28 Å
Radius of gyration Rg (electron density) rg_electron	11.77 Å
Forward intensity I(0) i0	399000000.00
Molecular weight molecular_weight	171700.0 kDa
Excluded volume excluded_volume	216590 Å³
Envelope volume envelope_volume	19679 Å³
Hydration-shell volume shell_volume	12033 Å³
Envelope diameter envelope_diameter	49.1 Å
Shell Rg shell_rg	19.96 Å
Envelope Rg envelope_rg	14.70 Å
Shape Rg shape_rg	11.74 Å
Total Rg total_rg	12.06 Å
Total atoms total_atoms	24600
Residues n_residues	1520
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	30.0 Å
Rg (real space) rg_real	11.74 Å
Rg uncertainty (real space) rg_real_error	0.02 Å
I(0) (real space) i0_real	3.8140e+08
I(0) uncertainty (real space) i0_real_error	2.4470e+06
Rg (reciprocal space) rg_reciprocal	12.22 Å
I(0) (reciprocal space) i0_reciprocal	399000000.0000
Solution quality estimate total_estimate	0.6822
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	16.4 Å
Skewness Skewness skewness	-0.122
Kurtosis Kurtosis kurtosis	-0.422
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	4.1120
Highest regularization parameter α highest_alpha	127300.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.992; Stabil: 0.965; Sysdev: 0.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1ud7a_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.1 — Ubiquitin-related

CATH v4.4 (1 domains)

Domain ID domain_id	1ud7A00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	1

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

Description description	PROTEIN (UBIQUITIN CORE MUTANT 1D7)
Molecular weight formula_weight	8596.8 kDa
Mutation mutation	I3V,V5L,I13V,L15I,I23V,V26F,I67L
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	24600

fit	/app/data/saxs_computation/ud/1ud7/1ud7.fit
pddf	/app/data/pr_computation/ud/1ud7/1ud7.pr.out
profile	/app/data/saxs_computation/ud/1ud7/1ud7.dat

SOLUTION STRUCTURE OF THE DESIGNED HYDROPHOBIC CORE MUTANT OF UBIQUITIN, 1D7

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

PROTEIN (UBIQUITIN CORE MUTANT 1D7)

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

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)