SAXSdb — 5mk3

▼

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

Tyrosine-protein phosphatase non-receptor type 23

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 A； UniProt 1–361	Not recorded	Charged multivesicular body protein 4c × 1 （Q96CF2）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；277 K；0.2 M Potassium thiocyanate, 0.1 M Bis-Tris propane pH 6.5, 20% PEG 3350	Resolution 2.00 Å R-free 0.235
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 1–361	Not recorded	Charged multivesicular body protein 4c × 1 （Q96CF2）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；277 K；0.2 M Potassium thiocyanate, 0.1 M Bis-Tris propane pH 6.5, 20% PEG 3350	Resolution 2.00 Å R-free 0.235
3	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 1–361	Not recorded	Charged multivesicular body protein 4c × 1 （Q96CF2）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；277 K；0.2 M Potassium thiocyanate, 0.1 M Bis-Tris propane pH 6.5, 20% PEG 3350	Resolution 2.00 Å R-free 0.235
4	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 1–361	Not recorded	Charged multivesicular body protein 4c × 1 （Q96CF2）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；277 K；0.2 M Potassium thiocyanate, 0.1 M Bis-Tris propane pH 6.5, 20% PEG 3350	Resolution 2.00 Å R-free 0.235

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 5MK3	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3RAU Crystal structure of the HD-PTP Bro1 domain Deposited 2011-03-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–361（360 aa） Fragment：UNP residues 2-361 Chain B 2–361（360 aa） Fragment：UNP residues 2-361	Not recorded	ACT ACETATE ION × 8 EDO 1,2-ETHANEDIOL × 2 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；0.1M MES pH5.5, 16% PEG3350, 0.3M Magnesium Acetate, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.95 Å R-free 0.215
5CRU Crystal structure of the Bro domain of HD-PTP Deposited 2015-07-23	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–361（361 aa） Fragment：UNP residues 1-361	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.3；293 K；0.03 M HEPES sodium, 16%(w/v) polyethylene glycol 3350, 0.67%(w/v) tryptone, 0.03 M urea	Resolution 2.40 Å R-free 0.259
5CRU Crystal structure of the Bro domain of HD-PTP Deposited 2015-07-23	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–361（361 aa） Fragment：UNP residues 1-361	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.3；293 K；0.03 M HEPES sodium, 16%(w/v) polyethylene glycol 3350, 0.67%(w/v) tryptone, 0.03 M urea	Resolution 2.40 Å R-free 0.259
5CRU Crystal structure of the Bro domain of HD-PTP Deposited 2015-07-23	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1–361（361 aa） Fragment：UNP residues 1-361	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.3；293 K；0.03 M HEPES sodium, 16%(w/v) polyethylene glycol 3350, 0.67%(w/v) tryptone, 0.03 M urea	Resolution 2.40 Å R-free 0.259
5CRU Crystal structure of the Bro domain of HD-PTP Deposited 2015-07-23	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 1–361（361 aa） Fragment：UNP residues 1-361	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.3；293 K；0.03 M HEPES sodium, 16%(w/v) polyethylene glycol 3350, 0.67%(w/v) tryptone, 0.03 M urea	Resolution 2.40 Å R-free 0.259
5CRV Crystal structure of the Bro domain of HD-PTP in a complex with the core region of STAM2 Deposited 2015-07-23	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–361（361 aa） Fragment：UNP residues 1-361	Mutation：N33A,Y34A	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；0.1 M Bis-Tris, 30%(w/v) polyethylene glycol 3350, 4%(v/v) acetonitrile	Resolution 2.00 Å R-free 0.241
5CRV Crystal structure of the Bro domain of HD-PTP in a complex with the core region of STAM2 Deposited 2015-07-23	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–361（361 aa） Fragment：UNP residues 1-361	Mutation：N33A,Y34A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；0.1 M Bis-Tris, 30%(w/v) polyethylene glycol 3350, 4%(v/v) acetonitrile	Resolution 2.00 Å R-free 0.241
5LM1 Crystal Structure of HD-PTP phosphatase in complex with UBAP1 Deposited 2016-07-28	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 362–713（352 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；0.2 M KSCN, 20% PEG3350	Resolution 2.55 Å R-free 0.254
5LM2 Crystal Structure of HD-PTP phosphatase Deposited 2016-07-28	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 362–713（352 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；0.1 M Bis-Tris pH 6.0, 0.1-0.2 M Na-Formate and 13-15% PEG3350	Resolution 2.54 Å R-free 0.271
5LM2 Crystal Structure of HD-PTP phosphatase Deposited 2016-07-28	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 362–713（352 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；0.1 M Bis-Tris pH 6.0, 0.1-0.2 M Na-Formate and 13-15% PEG3350	Resolution 2.54 Å R-free 0.271
5MJY Crystal structure of the His Domain Protein Tyrosine Phosphatase (HD-PTP/PTPN23) Bro1 domain (SARA complex structure) Deposited 2016-12-02	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–361（361 aa） Chain B 1–361（361 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；277 K；0.1 M MMT buffer pH 9.0, 25% PEG1500	Resolution 2.25 Å R-free 0.235
5MJY Crystal structure of the His Domain Protein Tyrosine Phosphatase (HD-PTP/PTPN23) Bro1 domain (SARA complex structure) Deposited 2016-12-02	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–361（361 aa） Chain D 1–361（361 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；277 K；0.1 M MMT buffer pH 9.0, 25% PEG1500	Resolution 2.25 Å R-free 0.235
5MJZ Crystal structure of the His Domain Protein Tyrosine Phosphatase (HD-PTP/PTPN23) Bro1 domain (Apo structure) Deposited 2016-12-02	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–361（361 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；277 K；Apo- HD-PTPBro1 crystals were obtained in 0.2M L-Na-Glutamate, 0.2M Alanine, 0.2M Glycine, 0.2M Lysine HCl, 0.2M Serine, 0.1 M Imidazole; MES monohydrate at pH 6.5 and 30% Ethylene glycol, PEG8K.	Resolution 1.87 Å R-free 0.216
5MJZ Crystal structure of the His Domain Protein Tyrosine Phosphatase (HD-PTP/PTPN23) Bro1 domain (Apo structure) Deposited 2016-12-02	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–361（361 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；277 K；Apo- HD-PTPBro1 crystals were obtained in 0.2M L-Na-Glutamate, 0.2M Alanine, 0.2M Glycine, 0.2M Lysine HCl, 0.2M Serine, 0.1 M Imidazole; MES monohydrate at pH 6.5 and 30% Ethylene glycol, PEG8K.	Resolution 1.87 Å R-free 0.216
5MK0 Crystal structure of the His Domain Protein Tyrosine Phosphatase (HD-PTP/PTPN23) Bro1 domain (Endofin peptide complex) Deposited 2016-12-02	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–361（361 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.2 M Ammonium tartrate dibasic, 20% PEG3350 and 0.1 M MMT buffer pH 9.0, 25% PEG1500	Resolution 1.76 Å R-free 0.193
5MK0 Crystal structure of the His Domain Protein Tyrosine Phosphatase (HD-PTP/PTPN23) Bro1 domain (Endofin peptide complex) Deposited 2016-12-02	Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–361（361 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.2 M Ammonium tartrate dibasic, 20% PEG3350 and 0.1 M MMT buffer pH 9.0, 25% PEG1500	Resolution 1.76 Å R-free 0.193
5MK1 Crystal structure of the His Domain Protein Tyrosine Phosphatase (HD-PTP/PTPN23) Bro1 domain (CHMP4A peptide complex structure) Deposited 2016-12-02	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–361（361 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；277 K；0.1 M Tris pH 7.8, 5% (poly-glutamic acid low molecular weight polymer) 20% PEG3350	Resolution 2.50 Å R-free 0.226
5MK1 Crystal structure of the His Domain Protein Tyrosine Phosphatase (HD-PTP/PTPN23) Bro1 domain (CHMP4A peptide complex structure) Deposited 2016-12-02	Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–361（361 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；277 K；0.1 M Tris pH 7.8, 5% (poly-glutamic acid low molecular weight polymer) 20% PEG3350	Resolution 2.50 Å R-free 0.226
5MK1 Crystal structure of the His Domain Protein Tyrosine Phosphatase (HD-PTP/PTPN23) Bro1 domain (CHMP4A peptide complex structure) Deposited 2016-12-02	Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–361（361 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；277 K；0.1 M Tris pH 7.8, 5% (poly-glutamic acid low molecular weight polymer) 20% PEG3350	Resolution 2.50 Å R-free 0.226
5MK1 Crystal structure of the His Domain Protein Tyrosine Phosphatase (HD-PTP/PTPN23) Bro1 domain (CHMP4A peptide complex structure) Deposited 2016-12-02	Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1–361（361 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；277 K；0.1 M Tris pH 7.8, 5% (poly-glutamic acid low molecular weight polymer) 20% PEG3350	Resolution 2.50 Å R-free 0.226
5MK2 Crystal structure of the His Domain Protein Tyrosine Phosphatase (HD-PTP/PTPN23) Bro1 domain (CHMP4B peptide complex structure) Deposited 2016-12-02	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–361（361 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；277 K；0.2 M CaCl2, 0.1 M MES pH 6.0, 20% PEG 6K	Resolution 1.70 Å R-free 0.203
5MK2 Crystal structure of the His Domain Protein Tyrosine Phosphatase (HD-PTP/PTPN23) Bro1 domain (CHMP4B peptide complex structure) Deposited 2016-12-02	Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–361（361 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；277 K；0.2 M CaCl2, 0.1 M MES pH 6.0, 20% PEG 6K	Resolution 1.70 Å R-free 0.203

10 other PDB entries and 22 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PTN23_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–361； UniProt 1–361 Author chain B； PDBConstruct 1–361； UniProt 1–361 Author chain C； PDBConstruct 1–361； UniProt 1–361 Author chain D； PDBConstruct 1–361； UniProt 1–361

Charged multivesicular body protein 4c

OrganismNot specified

UniProt Q96CF2

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 E； UniProt 216–233	Not recorded	Tyrosine-protein phosphatase non-receptor type 23 × 1 （Q9H3S7）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；277 K；0.2 M Potassium thiocyanate, 0.1 M Bis-Tris propane pH 6.5, 20% PEG 3350	Resolution 2.00 Å R-free 0.235
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain F； UniProt 216–233	Not recorded	Tyrosine-protein phosphatase non-receptor type 23 × 1 （Q9H3S7）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；277 K；0.2 M Potassium thiocyanate, 0.1 M Bis-Tris propane pH 6.5, 20% PEG 3350	Resolution 2.00 Å R-free 0.235
3	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain G； UniProt 216–233	Not recorded	Tyrosine-protein phosphatase non-receptor type 23 × 1 （Q9H3S7）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；277 K；0.2 M Potassium thiocyanate, 0.1 M Bis-Tris propane pH 6.5, 20% PEG 3350	Resolution 2.00 Å R-free 0.235
4	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain H； UniProt 216–233	Not recorded	Tyrosine-protein phosphatase non-receptor type 23 × 1 （Q9H3S7）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；277 K；0.2 M Potassium thiocyanate, 0.1 M Bis-Tris propane pH 6.5, 20% PEG 3350	Resolution 2.00 Å R-free 0.235

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 5MK3	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3C3R ALIX BRO1 CHMP4C complex Deposited 2008-01-28	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 221–233（13 aa）	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；10% PEG 2,000, 100mM Na MES pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.02 Å R-free 0.288
5V3R CHMP4C in complex with ALIX BRO1 Deposited 2017-03-08	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 216–233（18 aa） Fragment：C-terminal domain (UNP residues 216-233)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293.15 K；10% PEG20000, 100 mM MES, pH 6.5	Resolution 1.91 Å R-free 0.213
5WA1 CHMP4C A232T in complex with ALIX BRO1 Deposited 2017-06-24	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 216–233（18 aa） Fragment：UNP residues 216-233	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293.15 K；15% PEG8000, 100 mM MES, pH 6.5, 200 mM sodium acetate	Resolution 1.87 Å R-free 0.215

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

View Construct and Data Evidence

UniProt name	CHM4C_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain E； PDBConstruct 1–18； UniProt 216–233 Author chain F； PDBConstruct 1–18； UniProt 216–233 Author chain G； PDBConstruct 1–18； UniProt 216–233 Author chain H； PDBConstruct 1–18； UniProt 216–233

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	5mk3
Deposition date deposition_date	2016-12-02
Structure title title	Crystal structure of the His Domain Protein Tyrosine Phosphatase (HD-PTP/PTPN23) Bro 1 domain (CHMP4C peptide complex structure)
Keywords keywords	ESCRT-III CHMP4C, Hydrolase; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	39.96 Å
Radius of gyration Rg (electron density) rg_electron	39.63 Å
Forward intensity I(0) i0	408298000.00
Molecular weight molecular_weight	167320.0 kDa
Excluded volume excluded_volume	210750 Å³
Envelope volume envelope_volume	278360 Å³
Hydration-shell volume shell_volume	60188 Å³
Envelope diameter envelope_diameter	152.8 Å
Shell Rg shell_rg	44.02 Å
Envelope Rg envelope_rg	39.05 Å
Shape Rg shape_rg	39.63 Å
Total Rg total_rg	39.90 Å
Total atoms total_atoms	11762
Residues n_residues	1487
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

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	141.3 Å
Rg (real space) rg_real	40.00 Å
Rg uncertainty (real space) rg_real_error	1.31 Å
I(0) (real space) i0_real	4.0830e+08
I(0) uncertainty (real space) i0_real_error	7.3010e+06
Rg (reciprocal space) rg_reciprocal	39.97 Å
I(0) (reciprocal space) i0_reciprocal	408300000.0000
Solution quality estimate total_estimate	0.8618
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	45.9 Å
Skewness Skewness skewness	0.391
Kurtosis Kurtosis kurtosis	-0.180
Angular range angular_range	— – 0.2000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	31590000.0000
Real-space data points n_real_points	41
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.753; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.983; Smooth: 0.956

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Tyrosine-protein phosphatase non-receptor type 23
Molecular weight formula_weight	40719.9 kDa
EC 编号 ec_number	3.1.3.48
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	12582

MEAVPRMPMIWLDLKEAGDFHFQPAVKKFVLKNYGENPEAYNEELKKLELLRQNAVRVPRDFEGCSVLRKYLGQLHYLQSRVPMGSGQEAAVPVTWTEIFSGKSVAHEDIKYEQACILYNLGALHSMLGAMDKRVSEEGMKVSCTHFQCAAGAFAYLREHFPQAYSVDMSRQILTLNVNLMLGQAQECLLEKSMLDNRKSFLVARISAQVVDYYKEACRALENPDTASLLGRIQKDWKKLVQMKIYYFAAVAHLHMGKQAEEQQKFGERVAYFQSALDKLNEAIKLAKGQPDTVQDALRFTMDVIGGKYNSAKKDNDFIYHEAVPALDTLQPVKGAPLVKPLPVNPTDPAVTGPDIFAKLV

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 2 Entity 2 polymer

Description description	Charged multivesicular body protein 4c
Molecular weight formula_weight	2091.2 kDa
Source method src_method	syn
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,F,G,H

QRAEEEDDDIKQLAAWAT

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	780

▼

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	5mk3A00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	280 — alix/aip1 like domains

Domain ID domain_id	5mk3B00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	280 — alix/aip1 like domains

Domain ID domain_id	5mk3C00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	280 — alix/aip1 like domains

Domain ID domain_id	5mk3D00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	280 — alix/aip1 like domains

▶

8. Citations (1)

▶

Unit-cell length a length_a	66.436 Å
Unit-cell length b length_b	70.835 Å
Unit-cell length c length_c	79.291 Å
Unit-cell angle α angle_alpha	90.54 °
Unit-cell angle β angle_beta	98.22 °
Unit-cell angle γ angle_gamma	106.82 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	49.920 Å
R factor r_factor	0.1982
R_work r_work	0.1975
R_free r_free	0.2350

fit	/app/data/saxs_computation/mk/5mk3/5mk3.fit
pddf	/app/data/pr_computation/mk/5mk3/5mk3.pr.out
profile	/app/data/saxs_computation/mk/5mk3/5mk3.dat

Crystal structure of the His Domain Protein Tyrosine Phosphatase (HD-PTP/PTPN23) Bro 1 domain (CHMP4C peptide complex structure)

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

Tyrosine-protein phosphatase non-receptor type 23

State in the Current Structure

Other States of the Same Protein in the Database

Charged multivesicular body protein 4c

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

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)