SAXSdb — 2vsp

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

PDZ DOMAIN-CONTAINING PROTEIN 1

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 375–459	Fragment：FOURTH PDZ DOMAIN, RESIDUES 375-459	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：50% PEG 300; 0.20M NACL; 0.1M NA/K-PO4 PH 6.2	Resolution 2.41 Å R-free 0.267
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 375–459	Fragment：FOURTH PDZ DOMAIN, RESIDUES 375-459	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：50% PEG 300; 0.20M NACL; 0.1M NA/K-PO4 PH 6.2	Resolution 2.41 Å R-free 0.267
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 375–459	Fragment：FOURTH PDZ DOMAIN, RESIDUES 375-459	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：50% PEG 300; 0.20M NACL; 0.1M NA/K-PO4 PH 6.2	Resolution 2.41 Å R-free 0.267
4	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 375–459	Fragment：FOURTH PDZ DOMAIN, RESIDUES 375-459	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：50% PEG 300; 0.20M NACL; 0.1M NA/K-PO4 PH 6.2	Resolution 2.41 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 2VSP	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2EEI Solution Structure of Second PDZ domain of PDZ Domain Containing Protein 1 Deposited 2007-02-15	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 132–224（93 aa） Fragment：pdz domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient NMR sample composition 3.36mM PDZ domain U-13C,15N; 20mM d-Tris-HCl(pH 7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 10% D20, 90% H2O \| 10% D20, 90% H2O	Resolution not provided
2EEJ Solution Structure of Fourth PDZ domain of PDZ Domain Containing Protein 1 Deposited 2007-02-15	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 376–458（83 aa） Fragment：PDZ domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；296 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient NMR sample composition 2.65mM PDZ domain U-13C,15N; 20mM d-Tris-HCl(pH 7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 10% D20, 90% H2O \| 90% H2O/10% D2O	Resolution not provided
3TMH Crystal structure of dual-specific A-kinase anchoring protein 2 in complex with cAMP-dependent protein kinase A type II alpha and PDZK1 Deposited 2011-08-31	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: eicosameric	Chain A 375–459（85 aa） Fragment：UNP RESIDUES 375-459 Chain E 375–459（85 aa） Fragment：UNP RESIDUES 375-459 Chain I 375–459（85 aa） Fragment：UNP RESIDUES 375-459	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions MICROBATCH；pH 7；293 K；100 mM HEPES, pH 7, 20% PEG MME, Microbatch, temperature 293K	Resolution 3.80 Å R-free 0.328
4Q2P NHERF3 PDZ2 in Complex with a Phage-Derived Peptide Deposited 2014-04-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 132–215（84 aa） Fragment：unp residues 132-215 Chain B 132–215（84 aa） Fragment：unp residues 132-215 Chain C 132–215（84 aa） Fragment：unp residues 132-215	Not recorded	TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 4.6；292 K；30% PEG 4000, 0.1 M sodium acetate (pH 4.6), 0.1 M magnesium chloride, VAPOR DIFFUSION, temperature 292K	Resolution 2.05 Å R-free 0.252
6EZI PDZK1 domain 4 in complex with C-terminal peptide of human PepT2. Deposited 2017-11-15	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 374–460（87 aa）	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；292.15 K；0.1 M Trisodium citrate pH 6.45 20% PEG 4000 20 %(v/v) isopropanol	Resolution 1.50 Å R-free 0.214
9RXN Structure of the PDZ1 domain from human PDZK1 (NHERF3) with the C-terminal residues (KSTQF) of human URAT1 transporter (SLC22A12) Deposited 2025-07-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 6–106（101 aa）	Not recorded	NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.4；293 K；50 mM Bicine pH 8.4, 12% PEG 600, 3.5% PEG 2000 MME	Resolution 1.36 Å R-free 0.161
9RXN Structure of the PDZ1 domain from human PDZK1 (NHERF3) with the C-terminal residues (KSTQF) of human URAT1 transporter (SLC22A12) Deposited 2025-07-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 6–106（101 aa）	Not recorded	NA SODIUM ION × 1 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.4；293 K；50 mM Bicine pH 8.4, 12% PEG 600, 3.5% PEG 2000 MME	Resolution 1.36 Å R-free 0.161
9RXO Structure of the PDZ2 domain from human PDZK1 (NHERF3) with the C-terminal residues (KSTQF) of human URAT1 transporter (SLC22A12) Deposited 2025-07-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 131–215（85 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；26% PEG 1500	Resolution 1.20 Å R-free 0.203
9RXO Structure of the PDZ2 domain from human PDZK1 (NHERF3) with the C-terminal residues (KSTQF) of human URAT1 transporter (SLC22A12) Deposited 2025-07-11	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 131–215（85 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；26% PEG 1500	Resolution 1.20 Å R-free 0.203
9RXP Structure of the PDZ4 domain from human PDZK1 (NHERF3) with the C-terminal residues (KSTQF) of human URAT1 transporter (SLC22A12) Deposited 2025-07-11	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 375–458（84 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1% 2-methyl-2,4-pentanediol, 2.5 M ammonium sulfate	Resolution 1.43 Å R-free 0.231
9RXP Structure of the PDZ4 domain from human PDZK1 (NHERF3) with the C-terminal residues (KSTQF) of human URAT1 transporter (SLC22A12) Deposited 2025-07-11	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 375–458（84 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1% 2-methyl-2,4-pentanediol, 2.5 M ammonium sulfate	Resolution 1.43 Å R-free 0.231
9RXR Structure of the PDZ1 domain from human PDZK1 (NHERF3) with the C-terminal residues (VLKSTQF) of human URAT1 transporter (SLC22A12) Deposited 2025-07-11	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 6–106（101 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；100 mM MES, pH 6.5, 700 mM NaCl, 18% PEG 4000	Resolution 1.69 Å R-free 0.210
9RXS Structure of the PDZ4 domain from human PDZK1 (NHERF3) with the C-terminal residues (VLKSTQF) of human URAT1 transporter (SLC22A12) Deposited 2025-07-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 375–458（84 aa）	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；100 mM Tris pH 8.5, 100mM NaCl, 18% PEG 10000, 20% Glycerol	Resolution 2.00 Å R-free 0.242
9RXS Structure of the PDZ4 domain from human PDZK1 (NHERF3) with the C-terminal residues (VLKSTQF) of human URAT1 transporter (SLC22A12) Deposited 2025-07-11	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 375–458（84 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；100 mM Tris pH 8.5, 100mM NaCl, 18% PEG 10000, 20% Glycerol	Resolution 2.00 Å R-free 0.242

10 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PDZD1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–87； UniProt 375–459 Author chain B； PDBConstruct 3–87； UniProt 375–459 Author chain C； PDBConstruct 3–87； UniProt 375–459 Author chain D； PDBConstruct 3–87； UniProt 375–459

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	2vsp
Deposition date deposition_date	2008-04-28
Structure title title	Crystal structure of the fourth PDZ domain of PDZ domain-containing protein 1
Keywords keywords	PDZ, MEMBRANE, CYTOPLASM, PHOSPHOPROTEIN, TRANSPORT PROTEIN, CASP; TRANSPORT PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	21.53 Å
Radius of gyration Rg (electron density) rg_electron	20.66 Å
Forward intensity I(0) i0	19110600.00
Molecular weight molecular_weight	33408.0 kDa
Excluded volume excluded_volume	42072 Å³
Envelope volume envelope_volume	51765 Å³
Hydration-shell volume shell_volume	21151 Å³
Envelope diameter envelope_diameter	75.2 Å
Shell Rg shell_rg	26.86 Å
Envelope Rg envelope_rg	20.80 Å
Shape Rg shape_rg	20.65 Å
Total Rg total_rg	21.58 Å
Total atoms total_atoms	2351
Residues n_residues	329
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	74.8 Å
Rg (real space) rg_real	21.45 Å
Rg uncertainty (real space) rg_real_error	0.51 Å
I(0) (real space) i0_real	1.9110e+07
I(0) uncertainty (real space) i0_real_error	2.1650e+05
Rg (reciprocal space) rg_reciprocal	21.47 Å
I(0) (reciprocal space) i0_reciprocal	19110000.0000
Solution quality estimate total_estimate	0.8629
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.3 Å
Skewness Skewness skewness	0.259
Kurtosis Kurtosis kurtosis	-0.297
Angular range angular_range	— – 0.3700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7407000.0000
Real-space data points n_real_points	69
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.745; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.979; Smooth: 1.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2vspa_
Class class	b — All beta proteins
Fold Fold fold	b.36 — PDZ domain-like
Superfamily Superfamily superfamily	b.36.1 — PDZ domain-like
Family Family family	b.36.1.0 — automated matches

Domain ID domain_id	d2vspb_
Class class	b — All beta proteins
Fold Fold fold	b.36 — PDZ domain-like
Superfamily Superfamily superfamily	b.36.1 — PDZ domain-like
Family Family family	b.36.1.0 — automated matches

Domain ID domain_id	d2vspc_
Class class	b — All beta proteins
Fold Fold fold	b.36 — PDZ domain-like
Superfamily Superfamily superfamily	b.36.1 — PDZ domain-like
Family Family family	b.36.1.0 — automated matches

Domain ID domain_id	d2vspd_
Class class	b — All beta proteins
Fold Fold fold	b.36 — PDZ domain-like
Superfamily Superfamily superfamily	b.36.1 — PDZ domain-like
Family Family family	b.36.1.0 — automated matches

CATH v4.4 (4 domains)

Domain ID domain_id	2vspA00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	42 — Pdz3 Domain
Homologous superfamily homologous superfamily	10 — PDZ domain

Domain ID domain_id	2vspB00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	42 — Pdz3 Domain
Homologous superfamily homologous superfamily	10 — PDZ domain

Domain ID domain_id	2vspC00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	42 — Pdz3 Domain
Homologous superfamily homologous superfamily	10 — PDZ domain

Domain ID domain_id	2vspD00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	42 — Pdz3 Domain
Homologous superfamily homologous superfamily	10 — PDZ domain

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8. Citations (1)

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Unit-cell length a length_a	99.327 Å
Unit-cell length b length_b	99.327 Å
Unit-cell length c length_c	97.114 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	36

Space group space_group	H 3
Space-group number int_tables_number	146
Crystal system crystal_system	—

Resolution resolution	2.410 Å
Low-resolution limit resolution_low	28.670 Å
R factor r_factor	0.2170
R_work r_work	0.2150
R_free r_free	0.2670

Description description	PDZ DOMAIN-CONTAINING PROTEIN 1
Molecular weight formula_weight	9795.2 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	2466

Crystal structure of the fourth PDZ domain of PDZ domain-containing protein 1

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

PDZ DOMAIN-CONTAINING PROTEIN 1

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) 8 domains

SCOP 2.08 (4 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	104

fit	/app/data/saxs_computation/vs/2vsp/2vsp.fit
pddf	/app/data/pr_computation/vs/2vsp/2vsp.pr.out
profile	/app/data/saxs_computation/vs/2vsp/2vsp.dat