9rxs

Structure of the PDZ4 domain from human PDZK1 (NHERF3) with the C-terminal residues (VLKSTQF) of human URAT1 transporter (SLC22A12)

Method: X-RAY DIFFRACTION D_max: 53.2 Å Quality: REASONABLE

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

Na(+)/H(+) exchange regulatory cofactor NHE-RF3,Solute carrier family 22 member 12

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	Insufficient information Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 375–458	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
2	Insufficient information Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 375–458	Not recorded	No other associated polymer	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

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 9RXS	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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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

10 other PDB entries and 16 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 2–85； UniProt 375–458 Author chain B； PDBConstruct 2–85； UniProt 375–458

Na(+)/H(+) exchange regulatory cofactor NHE-RF3,Solute carrier family 22 member 12

Homo sapiens

UniProt Q96S37

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Insufficient information Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 547–553	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
2	Insufficient information Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 547–553	Not recorded	No other associated polymer	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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 9RXS	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8WJG Cryo-EM structure of URAT1(R477S) Deposited 2023-09-25	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–538（538 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
8WJQ Cryo-EM structure of URAT1(R477S)-Urate complex Deposited 2023-09-26	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 1–538（538 aa）	Not recorded	URC URIC ACID × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
9B1F Human urate transporter 1 URAT1 in apo state Deposited 2024-03-13	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 3–553（551 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 6.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
9B1G Human urate transporter 1 URAT1 in complex with dotinurad Deposited 2024-03-13	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 3–553（551 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 A1AIK dotinurad × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 6.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.70 Å
9B1H Human urate transporter 1 URAT1 in complex with lesinurad Deposited 2024-03-13	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 3–553（551 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 A1AIL lesinurad × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 6.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
9B1I Human urate transporter 1 URAT1 in complex with verinurad Deposited 2024-03-13	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 3–553（551 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 A1AIJ verinurad × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 6.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å
9B1J Urate bound human URAT1 in the inward-facing state Deposited 2024-03-13	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 3–553（551 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 URC URIC ACID × 1 PO4 PHOSPHATE ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 6.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
9B1K Urate bound human URAT1 in the occluded state Deposited 2024-03-13	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 3–553（551 aa）	Not recorded	URC URIC ACID × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 6.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
9B1L Urate bound human URAT1 in the outward-facing state. Deposited 2024-03-13	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 3–553（551 aa）	Not recorded	URC URIC ACID × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 6.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
9B1M Pyrazinoate bound human URAT1 in the inward-facing state (site1) Deposited 2024-03-13	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 3–553（551 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 VGL PYRAZINE-2-CARBOXYLIC ACID × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 6.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
9B1N Pyrazinoate bound human URAT1 in the inward-facing state (site2) Deposited 2024-03-13	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 3–553（551 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 VGL PYRAZINE-2-CARBOXYLIC ACID × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 6.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
9B1O Pyrazinoate bound human URAT1 in the inward-facing state (site3) Deposited 2024-03-13	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 3–553（551 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 VGL PYRAZINE-2-CARBOXYLIC ACID × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 6.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
9IRW Structure of human URAT1 bound with urate Deposited 2024-07-16	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 1–553（553 aa）	Not recorded	URC URIC ACID × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.26 Å
9IRX Structure of human URAT1 bound with benzbromarone Deposited 2024-07-16	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 1–553（553 aa）	Not recorded	R75 [3,5-bis(bromanyl)-4-oxidanyl-phenyl]-(2-ethyl-1-benzofuran-3-yl)methanone × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
9IRY Structure of human URAT1 bound with verinurad Deposited 2024-07-16	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 1–553（553 aa）	Not recorded	A1AIJ verinurad × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
9JDV Human URAT1 bound with Uric acid Deposited 2024-09-01	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 1–553（553 aa）	Not recorded	URC URIC ACID × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.32 Å
9JDY Human URAT1 bound with verinurad Deposited 2024-09-01	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 1–553（553 aa）	Not recorded	A1AIJ verinurad × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.23 Å
9JDZ Human URAT1 bound to lesinurad Deposited 2024-09-01	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 1–553（553 aa）	Not recorded	A1AIL lesinurad × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
9JE0 Human URAT1 bound to benzbromarone Deposited 2024-09-01	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 1–553（553 aa）	Not recorded	R75 [3,5-bis(bromanyl)-4-oxidanyl-phenyl]-(2-ethyl-1-benzofuran-3-yl)methanone × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.23 Å
9JE1 Human URAT1 bound to dotinurad Deposited 2024-09-01	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 1–553（553 aa）	Not recorded	A1AIK dotinurad × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
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 ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 549–553（5 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 ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 549–553（5 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 ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 549–553（5 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 experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 549–553（5 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 experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 549–553（5 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 experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 549–553（5 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
9RXQ Structure of the PDZ1 domain from human NHERF1 with the C-terminal residues (KSTQF) of human URAT1 transporter (SLC22A12) Deposited 2025-07-11	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 549–553（5 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.4；293 K；100 mM sodium acetate pH 4.8 200 mM ammonium acetate 24% PEG 4000	Resolution 1.38 Å R-free 0.183
9RXQ Structure of the PDZ1 domain from human NHERF1 with the C-terminal residues (KSTQF) of human URAT1 transporter (SLC22A12) Deposited 2025-07-11	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 549–553（5 aa）	Not recorded	ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.4；293 K；100 mM sodium acetate pH 4.8 200 mM ammonium acetate 24% PEG 4000	Resolution 1.38 Å R-free 0.183
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 experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 547–553（7 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
9US8 Structure of human URAT1 bound with sulfinpyrazone Deposited 2025-05-01	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 1–553（553 aa）	Not recorded	A1EAY Sulfinpyrazone × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.32 Å

26 other PDB entries and 30 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	S22AC_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 86–92； UniProt 547–553 Author chain B； PDBConstruct 86–92； UniProt 547–553

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.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9rxs
Deposition date deposition_date	2025-07-11
Structure title title	Structure of the PDZ4 domain from human PDZK1 (NHERF3) with the C-terminal residues (VLKSTQF) of human URAT1 transporter (SLC22A12)
Keywords keywords	Scaffold protein, PDZ domain, urate transporter, solute carrier, protein-protein interaction, NHERFs, PROTEIN BINDING; PROTEIN BINDING
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	20.07 Å
Radius of gyration Rg (electron density) rg_electron	19.30 Å
Forward intensity I(0) i0	7217560.00
Molecular weight molecular_weight	19858.0 kDa
Excluded volume excluded_volume	25114 Å³
Envelope volume envelope_volume	32945 Å³
Hydration-shell volume shell_volume	15073 Å³
Envelope diameter envelope_diameter	82.1 Å
Shell Rg shell_rg	24.52 Å
Envelope Rg envelope_rg	20.69 Å
Shape Rg shape_rg	19.34 Å
Total Rg total_rg	20.15 Å
Total atoms total_atoms	2839
Residues n_residues	183
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	53.2 Å
Rg (real space) rg_real	18.88 Å
Rg uncertainty (real space) rg_real_error	0.08 Å
I(0) (real space) i0_real	6.8570e+06
I(0) uncertainty (real space) i0_real_error	6.5920e+04
Rg (reciprocal space) rg_reciprocal	20.17 Å
I(0) (reciprocal space) i0_reciprocal	7217000.0000
Solution quality estimate total_estimate	0.6841
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	20.5 Å
Skewness Skewness skewness	0.263
Kurtosis Kurtosis kurtosis	-0.494
Angular range angular_range	— – 0.3950 Å⁻¹
Current regularization parameter α current_alpha	3.7610
Highest regularization parameter α highest_alpha	1229000.0000
Real-space data points n_real_points	71
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.002; Oscil: 0.987; Stabil: 0.978; Sysdev: 0.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Na(+)/H(+) exchange regulatory cofactor NHE-RF3,Solute carrier family 22 member 12
Molecular weight formula_weight	9924.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3018

GKPKLCRLAKGENGYGFHLNAIRGLPGSFIKEVQKGGPADLAGLEDEDVIIEVNGVNVLDEPYEKVVDRIQSSGKNVTLLVCGKKVLKSTQF

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 non-polymer

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

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	115

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8. Citations (2)

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Unit-cell length a length_a	52.404 Å
Unit-cell length b length_b	52.404 Å
Unit-cell length c length_c	195.771 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	16

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	tetragonal

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	24.320 Å
R factor r_factor	0.2002
R_work r_work	0.1979
R_free r_free	0.2416

fit	/app/data/saxs_computation/rx/9rxs/9rxs.fit
pddf	/app/data/pr_computation/rx/9rxs/9rxs.pr.out
profile	/app/data/saxs_computation/rx/9rxs/9rxs.dat

Structure of the PDZ4 domain from human PDZK1 (NHERF3) with the C-terminal residues (VLKSTQF) of human URAT1 transporter (SLC22A12)

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

Na(+)/H(+) exchange regulatory cofactor NHE-RF3,Solute carrier family 22 member 12

State in the Current Structure

Other States of the Same Protein in the Database

Na(+)/H(+) exchange regulatory cofactor NHE-RF3,Solute carrier family 22 member 12

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 non-polymer

Entity 3 Entity 3 water

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)