SAXSdb — 3c3o

▼

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

Programmed cell death 6-interacting 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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–359	Fragment：BRO1 domain (UNP residues 1-358)	Charged multivesicular body protein 4a peptide × 1 （Q9BY43） GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；15% PEG 8,000, 100mM Na MES pH 6.5, 200mM Na Acetate, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.15 Å R-free 0.284

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 3C3O	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2OEV Crystal structure of ALIX/AIP1 Deposited 2007-01-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–698（698 aa） Fragment：Bro1-V Domains, residues 1-698	Mutation：K268Y, K269Y	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；286 K；8% PEG 4000, 0.1M ammonium acetate, 0.1M magnesium acetate, 0.05M hepes, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 286K	Resolution 3.30 Å R-free 0.317
2OEW Structure of ALIX/AIP1 Bro1 Domain Deposited 2007-01-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–359（359 aa） Fragment：Bro1 Domain, residues 1-359	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；286 K；10% PEG 20000, 0.1M NaMES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 286K	Resolution 2.55 Å R-free 0.274
2OEX Structure of ALIX/AIP1 V Domain Deposited 2007-01-01	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 360–702（343 aa） Fragment：V Domain, residues 359-702 Chain B 360–702（343 aa） Fragment：V Domain, residues 359-702	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 VAPOR DIFFUSION, SITTING DROP；pH 8；277 K；14% PEG 3350, 0.16M magnesium formate, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.58 Å R-free 0.302
2OJQ Crystal structure of Alix V domain Deposited 2007-01-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 360–702（343 aa） Fragment：V domain, residues 360-702	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, HANGING DROP；pH 8.5；13-15% PEG 6000, 6-10% ethylene glycol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 100K	Resolution 2.87 Å R-free 0.318
2R02 Crystal Structure of ALIX/AIP1 in complex with the HIV-1 YPLTSL Late Domain Deposited 2007-08-17	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 2–698（697 aa） Fragment：ALIX Bro1-V domains	Mutation：K268Y,K269Y	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions sitting drop vapor diffusion；pH 5.9；286 K；0.20-0.25 M MgCl2, 7-10% PEG 4000, 0.1 M NaMES, pH 5.9, sitting drop vapor diffusion, temperature 286K	Resolution 2.60 Å R-free 0.285
2R03 Crystal Structure of ALIX/AIP1 in complex with the YPDL Late Domain Deposited 2007-08-17	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 2–698（697 aa） Fragment：ALIX Bro1-V domains	Mutation：K268Y,K269Y	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.9；286 K；0.20-0.25 M MgCl2, 7-10% PEG 4000, 0.1 M NaMES, pH 5.9, VAPOR DIFFUSION, SITTING DROP, temperature 286K	Resolution 2.59 Å R-free 0.286
2R05 Crystal Structure of ALIX/AIP1 in complex with the HIV-1 YPLASL Late Domain Deposited 2007-08-17	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 2–698（697 aa） Fragment：ALIX Bro1-V domains	Mutation：K268Y,K269Y	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.9；286 K；0.20-0.25 M MgCl2, 7-10% PEG 4000, 0.1 M NaMES, pH 5.9, VAPOR DIFFUSION, SITTING DROP, temperature 286K	Resolution 2.55 Å R-free 0.280
2XS1 Crystal Structure of ALIX in complex with the SIVmac239 PYKEVTEDL Late Domain Deposited 2010-09-24	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 1–698（698 aa） Fragment：BRO1-V DOMAINS, RESIDUES 1-698	Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.2；6.5% PEG4000, 0.2 MGCL2, 0.1M MES PH 6.2	Resolution 2.30 Å R-free 0.252
2XS8 Crystal Structure of ALIX in complex with the SIVagmTan-1 AYDPARKLL Late Domain Deposited 2010-09-24	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 1–698（698 aa） Fragment：BRO1-V DOMAINS, RESIDUES 1-698	Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.1；6.1% PEG4000, 0.2M MGCL2, 0.1M MES PH 6.1	Resolution 2.50 Å R-free 0.261
2ZNE Crystal structure of Zn2+-bound form of des3-23ALG-2 complexed with Alix ABS peptide Deposited 2008-04-22	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 C 799–814（16 aa） Fragment：ALG-2 binding site, residues 799-814	Mutation：C15S	ZN ZINC ION × 4 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；10% 2-propanol, 0.1M Cacodylate, 0.2M zinc acetate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.20 Å R-free 0.274
2ZNE Crystal structure of Zn2+-bound form of des3-23ALG-2 complexed with Alix ABS peptide Deposited 2008-04-22	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 799–814（16 aa） Fragment：ALG-2 binding site, residues 799-814	Mutation：C15S	ZN ZINC ION × 4 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；10% 2-propanol, 0.1M Cacodylate, 0.2M zinc acetate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.20 Å R-free 0.274
2ZNE Crystal structure of Zn2+-bound form of des3-23ALG-2 complexed with Alix ABS peptide Deposited 2008-04-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 799–814（16 aa） Fragment：ALG-2 binding site, residues 799-814 Chain D 799–814（16 aa） Fragment：ALG-2 binding site, residues 799-814	Mutation：C15S Mutation：C15S	ZN ZINC ION × 8 NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；10% 2-propanol, 0.1M Cacodylate, 0.2M zinc acetate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.20 Å R-free 0.274
3C3Q ALIX Bro1-domain:CHMIP4B co-crystal structure Deposited 2008-01-28	Different construct Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–359（359 aa） Fragment：BRO1 domain (UNP residues 1-359)	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；15% PEG 8,000, 100mM Na MES pH 6.5, 200mM Na Acetate, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.10 Å R-free 0.290
3C3R ALIX BRO1 CHMP4C complex Deposited 2008-01-28	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–359（359 aa） Fragment：BRO1 domain (UNP residues 1-359)	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
3E1R Midbody targeting of the ESCRT machinery by a non-canonical coiled-coil in CEP55 Deposited 2008-08-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 797–809（13 aa） Fragment：UNP residues 797-809	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；294 K；100 mM MES, 22% PEG 6000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.00 Å R-free 0.248
3WUV Structure basis of inactivating cell abscission with chimera peptide 2 Deposited 2014-05-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 796–809（14 aa）	Mutation：P796D/P807I/G808P/Y809P	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；295 K；0.8M ammonium sulfate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.79 Å R-free 0.227
3WUV Structure basis of inactivating cell abscission with chimera peptide 2 Deposited 2014-05-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain F 796–809（14 aa）	Mutation：P796D/P807I/G808P/Y809P	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；295 K；0.8M ammonium sulfate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.79 Å R-free 0.227
3WUV Structure basis of inactivating cell abscission with chimera peptide 2 Deposited 2014-05-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain I 796–809（14 aa）	Mutation：P796D/P807I/G808P/Y809P	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；295 K；0.8M ammonium sulfate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.79 Å R-free 0.227
3WUV Structure basis of inactivating cell abscission with chimera peptide 2 Deposited 2014-05-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain L 796–809（14 aa）	Mutation：P796D/P807I/G808P/Y809P	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；295 K；0.8M ammonium sulfate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.79 Å R-free 0.227
3WUV Structure basis of inactivating cell abscission with chimera peptide 2 Deposited 2014-05-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain O 796–809（14 aa）	Mutation：P796D/P807I/G808P/Y809P	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；295 K；0.8M ammonium sulfate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.79 Å R-free 0.227
3WUV Structure basis of inactivating cell abscission with chimera peptide 2 Deposited 2014-05-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain R 796–809（14 aa）	Mutation：P796D/P807I/G808P/Y809P	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；295 K；0.8M ammonium sulfate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.79 Å R-free 0.227
4JJY Alix V domain Deposited 2013-03-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 355–708（354 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, HANGING DROP；pH 5；277 K；0.1 M sodium citrate pH 5, 6-8% PEG 8000, 5-10% ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 6.50 Å R-free 0.283
4JJY Alix V domain Deposited 2013-03-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 355–708（354 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, HANGING DROP；pH 5；277 K；0.1 M sodium citrate pH 5, 6-8% PEG 8000, 5-10% ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 6.50 Å R-free 0.283
5V3R CHMP4C in complex with ALIX BRO1 Deposited 2017-03-08	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–359（359 aa）	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 mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–358（358 aa） Fragment：Bro1 domain (UNP residues 1-358)	Mutation：A232T	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
6KP3 STRUCTURE OF SENDAI VIRUS Y3/ALIX-BRO1 DOMAIN COMPLEX Deposited 2019-08-14	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–359（359 aa） Fragment：bro1 domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.45；297 K；15% PEG 3350, 0.2M Sodium Malonate-NaOH	Resolution 2.20 Å R-free 0.262

18 other PDB entries and 26 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PDC6I_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 22–380； UniProt 1–359

Charged multivesicular body protein 4a peptide

OrganismNot specified

UniProt Q9BY43

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 B； UniProt 210–222	Not recorded	Programmed cell death 6-interacting protein × 1 （Q8WUM4） GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；15% PEG 8,000, 100mM Na MES pH 6.5, 200mM Na Acetate, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.15 Å R-free 0.284

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 3C3O	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5MK1 Crystal structure of the His Domain Protein Tyrosine Phosphatase (HD-PTP/PTPN23) Bro1 domain (CHMP4A peptide complex structure) Deposited 2016-12-02	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 205–222（18 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 construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 205–222（18 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 construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 205–222（18 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 construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain K 205–222（18 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

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

View Construct and Data Evidence

UniProt name	CHM4A_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–13； UniProt 210–222

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	3c3o
Deposition date deposition_date	2008-01-28
Structure title title	ALIX Bro1-domain:CHMIP4A co-crystal structure
Keywords keywords	;CHMP4A ALIX BRO1 amphipathic-helix, Apoptosis, Host-virus interaction, Protein transport, Transport, Cytoplasmic vesicle, Lipid-binding, Membrane, TRANSPORT PROTEIN ;; TRANSPORT PROTEIN
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	26.03 Å
Radius of gyration Rg (electron density) rg_electron	25.55 Å
Forward intensity I(0) i0	27698700.00
Molecular weight molecular_weight	41397.0 kDa
Excluded volume excluded_volume	52289 Å³
Envelope volume envelope_volume	64424 Å³
Hydration-shell volume shell_volume	22834 Å³
Envelope diameter envelope_diameter	103.0 Å
Shell Rg shell_rg	30.32 Å
Envelope Rg envelope_rg	26.12 Å
Shape Rg shape_rg	25.56 Å
Total Rg total_rg	26.09 Å
Total atoms total_atoms	2916
Residues n_residues	370
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	98.0 Å
Rg (real space) rg_real	26.35 Å
Rg uncertainty (real space) rg_real_error	0.97 Å
I(0) (real space) i0_real	2.7700e+07
I(0) uncertainty (real space) i0_real_error	4.0300e+05
Rg (reciprocal space) rg_reciprocal	26.25 Å
I(0) (reciprocal space) i0_reciprocal	27700000.0000
Solution quality estimate total_estimate	0.7709
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.1 Å
Skewness Skewness skewness	0.685
Kurtosis Kurtosis kurtosis	0.112
Angular range angular_range	— – 0.3050 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7568000.0000
Real-space data points n_real_points	62
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.510; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.512; Smooth: 0.975

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Programmed cell death 6-interacting protein
Molecular weight formula_weight	42735.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3043

MHHHHHHHHHHSGQNLYFQGHMATFISVQLKKTSEVDLAKPLVKFIQQTYPSGGEEQAQYCRAAEELSKLRRAAVGRPLDKHEGALETLLRYYDQICSIEPKFPFSENQICLTFTWKDAFDKGSLFGGSVKLALASLGYEKSCVLFNCAALASQIAAEQNLDNDEGLKIAAKHYQFASGAFLHIKETVLSALSREPTVDISPDTVGTLSLIMLAQAQEVFFLKATRDKMKDAIIAKLANQAADYFGDAFKQCQYKDTLPKEVFPVLAAKHCIMQANAEYHQSILAKQQKKFGEEIARLQHAAELIKTVASRYDEYVNVKDFSDKINRALAAAKKDNDFIYHDRVPDLKDLDPIGKATLVKSTPVNVPISQKFTDLFEKMV

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Charged multivesicular body protein 4a peptide
Molecular weight formula_weight	1518.6 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

DEEALKQLAEWVS

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	127

▼

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	3c3oA00
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	120.668 Å
Unit-cell length b length_b	62.681 Å
Unit-cell length c length_c	76.124 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	122.13 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.150 Å
Low-resolution limit resolution_low	32.220 Å
R factor r_factor	0.2187
R_work r_work	0.2138
R_free r_free	0.2840

fit	/app/data/saxs_computation/c3/3c3o/3c3o.fit
pddf	/app/data/pr_computation/c3/3c3o/3c3o.pr.out
profile	/app/data/saxs_computation/c3/3c3o/3c3o.dat

ALIX Bro1-domain:CHMIP4A co-crystal structure

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

Programmed cell death 6-interacting protein

State in the Current Structure

Other States of the Same Protein in the Database

Charged multivesicular body protein 4a peptide

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

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)