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7l9x

Structure of VPS4B in complex with an allele-specific covalent inhibitor

Method: X-RAY DIFFRACTION Dmax: 81.7 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Vacuolar protein sorting-associated protein 4B

Homo sapiens

UniProt O75351

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 1–444 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

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 7L9X Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1WR0 Structural characterization of the MIT domain from human Vps4b Deposited 2004-10-07 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 1–77（77 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) 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
1XWI Crystal Structure of VPS4B Deposited 2004-11-01 Different construct Different ligand/ion 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–104（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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–86（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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics 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 ligand/ion 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

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 3–446； UniProt 1–444

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.

SAXS scattering curve SAXS Profile

SAXS profile for 7l9x

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7l9x
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7l9x
Deposition date deposition_date2021-01-05
Structure title titleStructure of VPS4B in complex with an allele-specific covalent inhibitor
Keywords keywordschemical Inhibitor, hydrolase, ATPase, AAA superfamily, PROTEIN TRANSPORT; PROTEIN TRANSPORT
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier25.41 Å
Radius of gyration Rg (electron density) rg_electron24.56 Å
Forward intensity I(0) i018015700.00
Molecular weight molecular_weight32465.0 kDa
Excluded volume excluded_volume40730 ų
Envelope volume envelope_volume54761 ų
Hydration-shell volume shell_volume19748 ų
Envelope diameter envelope_diameter83.4 Å
Shell Rg shell_rg29.96 Å
Envelope Rg envelope_rg24.64 Å
Shape Rg shape_rg24.54 Å
Total Rg total_rg25.29 Å
Total atoms total_atoms2286
Residues n_residues300
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax81.7 Å
Rg (real space) rg_real25.56 Å
Rg uncertainty (real space) rg_real_error0.55 Å
I(0) (real space) i0_real1.8020e+07
I(0) uncertainty (real space) i0_real_error2.6810e+05
Rg (reciprocal space) rg_reciprocal25.52 Å
I(0) (reciprocal space) i0_reciprocal18020000.0000
Solution quality estimate total_estimate0.8874
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary23.7 Å
Skewness Skewness skewness0.440
Kurtosis Kurtosis kurtosis-0.495
Angular range angular_range— – 0.3100 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha2348000.0000
Real-space data points n_real_points63
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.899; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.876; Smooth: 0.959
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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8. Citations (1)

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9. Files and Curves (10)