SAXSdb — 1wr0

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

SKD1 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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–77	Fragment：MIT DOMAIN	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 7；298 K；Ionic strength (raw mmCIF value) NaCl 50mM；Pressure 1 NMR sample composition：1mM protein U-15N; 20mM Tris buffer; 50mM NaCl; 95% H2O, 5% D2O; 1mM DTT \| 95% H2O/5% D2O NMR sample composition：1mM protein U-15N,13C; 20mM Tris buffer; 50mM NaCl; 95% H2O, 5% D2O; 1mM DTT \| 95% H2O/5% D2O	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 1WR0	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1XWI Crystal Structure of VPS4B Deposited 2004-11-01	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 123–444（322 aa） Fragment：residues 123-444	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；300 K；Ammonium Sulfate, HEPES, NaCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K, pH 7.50	Resolution 2.80 Å R-free 0.260
2CPT Solution structure of MIT domain from human SKD1 Deposited 2005-05-19	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–104（104 aa） Fragment：MIT domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 100mM NaCl；Pressure ambient NMR sample composition 1.11mM 13C, 15N-labeled protein; 20mM d-Tris-HCl; 100mM NaCl; 1mM d10-DTT; 0.02% NaN3 \| 90% H2O/10% D2O	Resolution not provided
2JQH VPS4B MIT Deposited 2007-06-01	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–86（86 aa） Fragment：MIT domain, residues 1-86	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.65；298 K；Ionic strength (raw mmCIF value) 50；Pressure ambient NMR sample composition 1.8 mM [U-100% 13C; U-100% 15N] VPS4B MIT, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2JQK VPS4B MIT-CHMP2B Complex Deposited 2007-06-02	Different construct Different oligomeric state Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–86（86 aa） Fragment：MIT domain, residues 1-86	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.65；298 K；Ionic strength (raw mmCIF value) 50；Pressure ambient NMR sample composition 0.48 mM [U-100% 13C; U-100% 15N] VPS4B MIT, 4.8 mM CHMP2B(195-213), 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 2.84 mM VPS4B MIT, 0.26 mM [U-100% 13C; U-100% 15N] CHMP2B(195-213), 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
4U7Y Structure of the complex of VPS4B MIT and IST1 MIM Deposited 2014-07-31	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–89（89 aa） Fragment：MIT domain (UNP residues 1-89)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.3；299 K；2.58 M Na-malonate	Resolution 2.50 Å R-free 0.271
7L9X Structure of VPS4B in complex with an allele-specific covalent inhibitor Deposited 2021-01-05	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–444（444 aa）	Not recorded	XQV N-{3-[(8-phenyl[1,2,4]triazolo[1,5-a]pyridin-2-yl)amino]phenyl}propanamide × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291.15 K；100 mM NH4SO4, 100 mM Hepes pH 7.5, 10% PEG 4000	Resolution 2.81 Å R-free 0.267

6 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	VPS4B_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–81； UniProt 1–77

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	1wr0
Deposition date deposition_date	2004-10-07
Structure title title	Structural characterization of the MIT domain from human Vps4b
Keywords keywords	;VPS4b, SKD1, MIT DOMAIN, ESCORT, MVB, SNPs, PROTEIN TRANSPORT, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI ;; PROTEIN TRANSPORT
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	14.58 Å
Radius of gyration Rg (electron density) rg_electron	14.19 Å
Forward intensity I(0) i0	493117000.00
Molecular weight molecular_weight	183850.0 kDa
Excluded volume excluded_volume	228560 Å³
Envelope volume envelope_volume	26184 Å³
Hydration-shell volume shell_volume	13196 Å³
Envelope diameter envelope_diameter	63.5 Å
Shell Rg shell_rg	23.01 Å
Envelope Rg envelope_rg	18.73 Å
Shape Rg shape_rg	14.16 Å
Total Rg total_rg	14.47 Å
Total atoms total_atoms	25700
Residues n_residues	1620
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	58.5 Å
Rg (real space) rg_real	14.70 Å
Rg uncertainty (real space) rg_real_error	0.54 Å
I(0) (real space) i0_real	4.9310e+08
I(0) uncertainty (real space) i0_real_error	6.5290e+06
Rg (reciprocal space) rg_reciprocal	14.69 Å
I(0) (reciprocal space) i0_reciprocal	493100000.0000
Solution quality estimate total_estimate	0.5460
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	14.8 Å
Skewness Skewness skewness	0.539
Kurtosis Kurtosis kurtosis	-0.039
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	215400.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.336; Stabil: 1.000; Sysdev: 0.256; Positv: 1.000; Valcen: 0.321; Smooth: 0.996

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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) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1wr0a1
Class class	a — All alpha proteins
Fold Fold fold	a.7 — Spectrin repeat-like
Superfamily Superfamily superfamily	a.7.14 — MIT domain
Family Family family	a.7.14.1 — MIT domain

Domain ID domain_id	d1wr0a2
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 (1 domains)

Domain ID domain_id	1wr0A01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	80 — Phosphotransferase system, lactose/cellobiose-type IIA subunit

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8. Citations (1)

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Description description	SKD1 protein
Molecular weight formula_weight	9207.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	25700

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)

fit	/app/data/saxs_computation/wr/1wr0/1wr0.fit
pddf	/app/data/pr_computation/wr/1wr0/1wr0.pr.out
profile	/app/data/saxs_computation/wr/1wr0/1wr0.dat

Structural characterization of the MIT domain from human Vps4b

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

SKD1 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

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)