SAXSdb — 6ezi

▼

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

Na(+)/H(+) exchange regulatory cofactor NHE-RF3

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 374–460	Not recorded	Solute carrier family 15 member 2 × 1 （Q16348） 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

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 6EZI	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 oligomeric state 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 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 oligomeric state 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 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
2VSP Crystal structure of the fourth PDZ domain of PDZ domain-containing protein 1 Deposited 2008-04-28	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 375–459（85 aa） Fragment：FOURTH PDZ DOMAIN, RESIDUES 375-459	Not recorded	No recorded non-water small molecule	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
2VSP Crystal structure of the fourth PDZ domain of PDZ domain-containing protein 1 Deposited 2008-04-28	Different construct 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 375–459（85 aa） Fragment：FOURTH PDZ DOMAIN, RESIDUES 375-459	Not recorded	No recorded non-water small molecule	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
2VSP Crystal structure of the fourth PDZ domain of PDZ domain-containing protein 1 Deposited 2008-04-28	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 375–459（85 aa） Fragment：FOURTH PDZ DOMAIN, RESIDUES 375-459	Not recorded	No recorded non-water small molecule	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
2VSP Crystal structure of the fourth PDZ domain of PDZ domain-containing protein 1 Deposited 2008-04-28	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 375–459（85 aa） Fragment：FOURTH PDZ DOMAIN, RESIDUES 375-459	Not recorded	No recorded non-water small molecule	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
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 ligand/ion 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
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 ligand/ion 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 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	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 ligand/ion 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 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	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 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 ligand/ion 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 17 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NHRF3_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–89； UniProt 374–460

Solute carrier family 15 member 2

OrganismNot specified

UniProt Q16348

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 720–729	Not recorded	Na(+)/H(+) exchange regulatory cofactor NHE-RF3 × 1 （Q5T2W1） 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

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 6EZI	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7PMY HsPepT2 bound to Ala-Phe in the inward facing partially occluded conformation Deposited 2021-09-04	Different construct 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 1–729（729 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen PROPANE	Resolution 3.80 Å
9UDC Cryo-EM Structure of SLC15A2 with NAD+ (Pose 1) Deposited 2025-04-06	Different construct Different oligomeric state 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 1–729（729 aa）	Not recorded	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.38 Å

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	S15A2_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–10； UniProt 720–729

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	6ezi
Deposition date deposition_date	2017-11-15
Structure title title	PDZK1 domain 4 in complex with C-terminal peptide of human PepT2.
Keywords keywords	PDZK1 Human peptide transporter Na(+)-H(+) exchange regulatory cofactor NHE-RF3 Protein complex binding, PROTEIN BINDING; PROTEIN BINDING
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	13.44 Å
Radius of gyration Rg (electron density) rg_electron	12.07 Å
Forward intensity I(0) i0	2031030.00
Molecular weight molecular_weight	9920.0 kDa
Excluded volume excluded_volume	12559 Å³
Envelope volume envelope_volume	13859 Å³
Hydration-shell volume shell_volume	9861 Å³
Envelope diameter envelope_diameter	43.6 Å
Shell Rg shell_rg	17.67 Å
Envelope Rg envelope_rg	12.48 Å
Shape Rg shape_rg	12.04 Å
Total Rg total_rg	13.57 Å
Total atoms total_atoms	696
Residues n_residues	94
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	44.5 Å
Rg (real space) rg_real	13.34 Å
Rg uncertainty (real space) rg_real_error	0.25 Å
I(0) (real space) i0_real	2.0310e+06
I(0) uncertainty (real space) i0_real_error	2.1850e+04
Rg (reciprocal space) rg_reciprocal	13.35 Å
I(0) (reciprocal space) i0_reciprocal	2031000.0000
Solution quality estimate total_estimate	0.7866
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	18.0 Å
Skewness Skewness skewness	0.074
Kurtosis Kurtosis kurtosis	-0.278
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	444700.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.742; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.000

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Na(+)/H(+) exchange regulatory cofactor NHE-RF3
Molecular weight formula_weight	9653.1 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	917

SMHKPKLCRLAKGENGYGFHLNAIRGLPGSFIKEVQKGGPADLAGLEDEDVIIEVNGVNVLDEPYEKVVDRIQSSGKNVTLLVCGKKAY

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 BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Solute carrier family 15 member 2
Molecular weight formula_weight	1205.5 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

IKLETKKTKL

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	124

▼

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	6eziA00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	42 — Pdz3 Domain
Homologous superfamily homologous superfamily	10 — PDZ domain

▶

8. Citations (1)

▶

Unit-cell length a length_a	54.400 Å
Unit-cell length b length_b	54.400 Å
Unit-cell length c length_c	150.760 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	12

Space group space_group	P 65 2 2
Space-group number int_tables_number	179
Crystal system crystal_system	—

Resolution resolution	1.503 Å
Low-resolution limit resolution_low	47.112 Å
R factor r_factor	0.1948
R_work r_work	0.1938
R_free r_free	0.2142

fit	/app/data/saxs_computation/ez/6ezi/6ezi.fit
pddf	/app/data/pr_computation/ez/6ezi/6ezi.pr.out
profile	/app/data/saxs_computation/ez/6ezi/6ezi.dat

PDZK1 domain 4 in complex with C-terminal peptide of human PepT2.

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

Na(+)/H(+) exchange regulatory cofactor NHE-RF3

State in the Current Structure

Other States of the Same Protein in the Database

Solute carrier family 15 member 2

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 (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)