SAXSdb — 2yps

▼

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

SORTING NEXIN-3

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 24–155	Fragment：PX DOMAIN, RESIDUES 24-155	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：3.5M FORMATE	Resolution 2.60 Å R-free 0.255
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 24–155	Fragment：PX DOMAIN, RESIDUES 24-155	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：3.5M FORMATE	Resolution 2.60 Å R-free 0.255
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 24–155	Fragment：PX DOMAIN, RESIDUES 24-155	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：3.5M FORMATE	Resolution 2.60 Å R-free 0.255
4	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 24–155	Fragment：PX DOMAIN, RESIDUES 24-155	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：3.5M FORMATE	Resolution 2.60 Å R-free 0.255

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 2YPS	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2MXC Solution structure of the full length sorting nexin 3 Deposited 2014-12-20	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–162（161 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 0.100；Pressure 1.000 NMR sample composition 0.5 mM [U-100% 13C; U-100% 15N] SNX3FL, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
5F0J Structure of retromer VPS26-VPS35 subunits bound to SNX3 Deposited 2015-11-27	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 1–162（162 aa）	Not recorded	SO4 SULFATE ION × 6 GOL GLYCEROL × 5 EDO 1,2-ETHANEDIOL × 24	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；0.9 M AmSO4, 0.1 M MES pH 6.0	Resolution 2.70 Å R-free 0.246
5F0L Structure of retromer VPS26-VPS35 subunits bound to SNX3 and DMT1 Deposited 2015-11-27	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 1–162（162 aa） Fragment：Residues 14-470	Not recorded	SO4 SULFATE ION × 10 GOL GLYCEROL × 6 EDO 1,2-ETHANEDIOL × 18	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；0.75 M AmSO4, 0.1 M MES pH 6.0, 15% Glycerol	Resolution 3.20 Å R-free 0.259
5F0M Structure of retromer VPS26-VPS35 subunits bound to SNX3 and DMT1 (SeMet labeled) Deposited 2015-11-27	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 1–162（162 aa） Fragment：Residues 14-470	Not recorded	SO4 SULFATE ION × 6 GOL GLYCEROL × 5 EDO 1,2-ETHANEDIOL × 12	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；0.8 M AmSO4, 0.1 M MES pH 6.0, 5% Glycerol	Resolution 3.10 Å R-free 0.254
5F0P Structure of retromer VPS26-VPS35 subunits bound to SNX3 and DMT1(L557M) (SeMet labeled) Deposited 2015-11-27	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 1–162（162 aa） Fragment：Residues 1-162	Not recorded	SO4 SULFATE ION × 6 GOL GLYCEROL × 4 EDO 1,2-ETHANEDIOL × 20 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；0.8 M AmSO4, 0.1 M MES pH 6.0, 10% Glycerol	Resolution 2.78 Å R-free 0.261

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SNX3_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–134； UniProt 24–155 Author chain B； PDBConstruct 3–134； UniProt 24–155 Author chain C； PDBConstruct 3–134； UniProt 24–155 Author chain D； PDBConstruct 3–134； UniProt 24–155

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	2yps
Deposition date deposition_date	2012-10-31
Structure title title	Crystal structure of the PX domain of human sorting nexin 3
Keywords keywords	PROTEIN TRANSPORT, ENDOSOME; PROTEIN TRANSPORT
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	23.60 Å
Radius of gyration Rg (electron density) rg_electron	22.81 Å
Forward intensity I(0) i0	31333900.00
Molecular weight molecular_weight	43650.0 kDa
Excluded volume excluded_volume	54931 Å³
Envelope volume envelope_volume	68705 Å³
Hydration-shell volume shell_volume	25183 Å³
Envelope diameter envelope_diameter	78.4 Å
Shell Rg shell_rg	29.83 Å
Envelope Rg envelope_rg	22.63 Å
Shape Rg shape_rg	22.81 Å
Total Rg total_rg	23.72 Å
Total atoms total_atoms	3092
Residues n_residues	407
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	76.0 Å
Rg (real space) rg_real	23.93 Å
Rg uncertainty (real space) rg_real_error	0.18 Å
I(0) (real space) i0_real	3.0850e+07
I(0) uncertainty (real space) i0_real_error	3.3850e+05
Rg (reciprocal space) rg_reciprocal	23.50 Å
I(0) (reciprocal space) i0_reciprocal	31330000.0000
Solution quality estimate total_estimate	0.6944
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	32.1 Å
Skewness Skewness skewness	0.251
Kurtosis Kurtosis kurtosis	-0.288
Angular range angular_range	— – 0.3350 Å⁻¹
Current regularization parameter α current_alpha	5.9810
Highest regularization parameter α highest_alpha	11060000.0000
Real-space data points n_real_points	65
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.907; Stabil: 0.925; Sysdev: 0.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.559

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (2)

▼

7. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (5 domains)

Domain ID domain_id	d2ypsa1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.189 — PX domain
Superfamily Superfamily superfamily	d.189.1 — PX domain
Family Family family	d.189.1.0 — automated matches

Domain ID domain_id	d2ypsa2
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

Domain ID domain_id	d2ypsb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.189 — PX domain
Superfamily Superfamily superfamily	d.189.1 — PX domain
Family Family family	d.189.1.0 — automated matches

Domain ID domain_id	d2ypsc_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.189 — PX domain
Superfamily Superfamily superfamily	d.189.1 — PX domain
Family Family family	d.189.1.0 — automated matches

Domain ID domain_id	d2ypsd_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.189 — PX domain
Superfamily Superfamily superfamily	d.189.1 — PX domain
Family Family family	d.189.1.0 — automated matches

CATH v4.4 (4 domains)

Domain ID domain_id	2ypsA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1520 — PX Domain
Homologous superfamily homologous superfamily	10 — Phox-like domain

Domain ID domain_id	2ypsB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1520 — PX Domain
Homologous superfamily homologous superfamily	10 — Phox-like domain

Domain ID domain_id	2ypsC00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1520 — PX Domain
Homologous superfamily homologous superfamily	10 — Phox-like domain

Domain ID domain_id	2ypsD00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1520 — PX Domain
Homologous superfamily homologous superfamily	10 — Phox-like domain

▶

8. Citations (1)

▶

Unit-cell length a length_a	69.840 Å
Unit-cell length b length_b	81.700 Å
Unit-cell length c length_c	184.460 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	32

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	51.020 Å
R factor r_factor	0.2131
R_work r_work	0.2109
R_free r_free	0.2551

Description description	SORTING NEXIN-3
Molecular weight formula_weight	15652.8 kDa
Source method src_method	man
Copy count entity_count	4

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	3102

Crystal structure of the PX domain of human sorting nexin 3

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

SORTING NEXIN-3

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (5 domains)

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

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

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	10

fit	/app/data/saxs_computation/yp/2yps/2yps.fit
pddf	/app/data/pr_computation/yp/2yps/2yps.pr.out
profile	/app/data/saxs_computation/yp/2yps/2yps.dat