SAXSdb — 9n9y

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

WD repeat-containing protein 48

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 1–563	Fragment：residues 1-563	Ubiquitin carboxyl-terminal hydrolase 1, N-terminal fragment,Ubiquitin carboxyl-terminal hydrolase 1 × 1 （O94782） ZN ZINC ION × 1 A1BWW 2-(4-cyclopropyl-6-methoxypyrimidin-5-yl)-7-({4-[1-methyl-4-(trifluoromethyl)-1H-imidazol-2-yl]phenyl}methyl)-5H-pyrrolo[3,2-d]pyrimidine × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；1M sodium citrate (pH 6.5)	Resolution 3.15 Å R-free 0.291

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 9N9Y	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5CVL WDR48 (UAF-1), residues 2-580 Deposited 2015-07-27	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 2–580（579 aa） Fragment：UNP residues 2-580	Not recorded	PO4 PHOSPHATE ION × 2 AU GOLD ION × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；292 K；0.72 M sodium phosphate, 0.72 M potassium phosphate, 90 mM HEPES pH 7.5	Resolution 3.00 Å R-free 0.233
5CVN WDR48 (2-580):USP46~ubiquitin ternary complex Deposited 2015-07-27	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 A 2–580（579 aa） Fragment：UNP residues 2-580	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.8；292 K；0.1 M sodium chloride, 5% ethanol, 15% MPD, 0.1 M Tris pH 8.8	Resolution 3.36 Å R-free 0.222
5CVO WDR48:USP46~ubiquitin ternary complex Deposited 2015-07-27	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 A 1–677（677 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；292 K；15% MPD, 0.1 M NaCl, 0.1 M HEPES, pH 7.0	Resolution 3.88 Å R-free 0.275
5CVO WDR48:USP46~ubiquitin ternary complex Deposited 2015-07-27	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 1–677（677 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；292 K；15% MPD, 0.1 M NaCl, 0.1 M HEPES, pH 7.0	Resolution 3.88 Å R-free 0.275
5K1A Crystal structure of the UAF1-USP12 complex in C2 space group Deposited 2016-05-18	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–677（677 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；277 K；0.1 M sodium citrate, 7% PEG 3350, 0.15 M NaCl	Resolution 2.30 Å R-free 0.239
5K1A Crystal structure of the UAF1-USP12 complex in C2 space group Deposited 2016-05-18	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1–677（677 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；277 K；0.1 M sodium citrate, 7% PEG 3350, 0.15 M NaCl	Resolution 2.30 Å R-free 0.239
5K1A Crystal structure of the UAF1-USP12 complex in C2 space group Deposited 2016-05-18	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 1–677（677 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；277 K；0.1 M sodium citrate, 7% PEG 3350, 0.15 M NaCl	Resolution 2.30 Å R-free 0.239
5K1A Crystal structure of the UAF1-USP12 complex in C2 space group Deposited 2016-05-18	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 1–677（677 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；277 K；0.1 M sodium citrate, 7% PEG 3350, 0.15 M NaCl	Resolution 2.30 Å R-free 0.239
5K1B Crystal structure of the UAF1/USP12 complex in F222 space group Deposited 2016-05-18	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–677（677 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；277 K；0.1 M imidazole, 18% PEG 2000MME, 0.3 M ammonium citrate	Resolution 3.30 Å R-free 0.286
5K1C Crystal structure of the UAF1/WDR20/USP12 complex Deposited 2016-05-18	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–563（563 aa） Fragment：residues 1-563	Not recorded	ZN ZINC ION × 1 PO4 PHOSPHATE ION × 1 TAM TRIS(HYDROXYETHYL)AMINOMETHANE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；277 K；0.1 M MES, 1.3 M ammonium phosphate dibasic	Resolution 3.00 Å R-free 0.271
5L8E Structure of UAF1 Deposited 2016-06-07	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 9–580（572 aa）	Not recorded	GOL GLYCEROL × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；20% PEG3350, 200mM Tri-Sodium Citrate, Bis-Tris Propane Cryo -30% Glycerol	Resolution 2.30 Å R-free 0.224
5L8E Structure of UAF1 Deposited 2016-06-07	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 9–580（572 aa）	Not recorded	GOL GLYCEROL × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；20% PEG3350, 200mM Tri-Sodium Citrate, Bis-Tris Propane Cryo -30% Glycerol	Resolution 2.30 Å R-free 0.224
5L8W Structure of USP12-UB-PRG/UAF1 Deposited 2016-06-08	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 B 9–580（572 aa）	Not recorded	ZN ZINC ION × 1 GOL GLYCEROL × 1 AYE prop-2-en-1-amine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；3.2% PEG4000, 0.1mM MMT pH6.5, 0.1 mM TCEP. Cryo- 30% Glycerol	Resolution 2.79 Å R-free 0.259
6JLQ Crystal structure of human USP46-WDR48-WDR20 complex Deposited 2019-03-06	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–580（580 aa）	Not recorded	ZN ZINC ION × 1 GOL GLYCEROL × 8 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；1.0M Sodium phosphate monobasic monohydrate, Potassium phosphate dibasic, pH 7.2	Resolution 3.10 Å R-free 0.272
7AY0 Crystal structure of truncated USP1-UAF1 Deposited 2020-11-10	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–563（563 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；10% w/v PEG4000, 100 mM MES/Imidazole pH 6.0-6.5, 30 mM CaCl2, 30 mM MgCl2, 20-25% glycerol v/v	Resolution 3.60 Å R-free 0.266
7AY0 Crystal structure of truncated USP1-UAF1 Deposited 2020-11-10	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–563（563 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；10% w/v PEG4000, 100 mM MES/Imidazole pH 6.0-6.5, 30 mM CaCl2, 30 mM MgCl2, 20-25% glycerol v/v	Resolution 3.60 Å R-free 0.266
7AY1 Cryo-EM structure of USP1-UAF1 bound to mono-ubiquitinated FANCD2, and FANCI Deposited 2020-11-10	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: heptameric	Chain E 1–677（677 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å
7AY2 Crystal structure of truncated USP1-UAF1 reacted with ubiquitin-prg Deposited 2020-11-10	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 A 1–563（563 aa）	Not recorded	ZN ZINC ION × 1 AYE prop-2-en-1-amine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；8-13% w/v PEG3350, 0.1 M citric acid/Bis-Tris propane pH 4.1	Resolution 3.20 Å R-free 0.234
7AY2 Crystal structure of truncated USP1-UAF1 reacted with ubiquitin-prg Deposited 2020-11-10	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 1–563（563 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；8-13% w/v PEG3350, 0.1 M citric acid/Bis-Tris propane pH 4.1	Resolution 3.20 Å R-free 0.234
8A9J Cryo-EM structure of USP1-UAF1 bound to FANCI and mono-ubiquitinated FANCD2 without ML323 (consensus reconstruction) Deposited 2022-06-28	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: heptameric	Chain E 1–677（677 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；blotted for 3.0 secs before plunging	Resolution 2.80 Å
8A9K Cryo-EM structure of USP1-UAF1 bound to FANCI and mono-ubiquitinated FANCD2 with ML323 (consensus reconstruction) Deposited 2022-06-28	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: heptameric	Chain E 1–677（677 aa）	Not recorded	ZN ZINC ION × 1 JDA 5-methyl-2-(2-propan-2-ylphenyl)-~{N}-[[4-(1,2,3-triazol-1-yl)phenyl]methyl]pyrimidin-4-amine × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.85 Å
9DI1 Cryo-EM structure of the USP1-UAF1-Ubiquitin complex inhibited by KSQ-4279 Deposited 2024-09-04	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–677（677 aa）	Not recorded	ZN ZINC ION × 1 A1IB8 6-(4-cyclopropyl-6-methoxy-pyrimidin-5-yl)-1-[[4-[1-propan-2-yl-4-(trifluoromethyl)imidazol-2-yl]phenyl]methyl]pyrazolo[3,4-d]pyrimidine × 1 A1A4Y 3-(methanesulfonyl)propan-1-amine × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.70 Å
9DI2 Cryo-EM structure of the USP1-UAF1-Ubiquitin-VS complex Deposited 2024-09-04	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–677（677 aa）	Not recorded	ZN ZINC ION × 1 A1A4Y 3-(methanesulfonyl)propan-1-amine × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.60 Å
9EBS Cryo-EM structure of USP1-UAF1-Ubiquitin in complex with TNG348 Deposited 2024-11-13	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 1–677（677 aa）	Not recorded	A1A4Y 3-(methanesulfonyl)propan-1-amine × 1 ZN ZINC ION × 1 A1BHF 2-(4-cyclopropyl-6-methoxypyrimidin-5-yl)-9-({4-[1-methyl-4-(trifluoromethyl)-1H-imidazol-2-yl]phenyl}methyl)-7-(2,2,2-trifluoroethyl)-7,9-dihydro-8H-purin-8-imine × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
9HNW USP1-UAF1 bound to Lys63-linked diubiquitin Deposited 2024-12-11	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–672（672 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.04 Å

18 other PDB entries and 25 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	WDR48_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–563； UniProt 1–563

Ubiquitin carboxyl-terminal hydrolase 1, N-terminal fragment,Ubiquitin carboxyl-terminal hydrolase 1

Homo sapiens

UniProt O94782

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 85–222 Chain B； UniProt 421–605 Chain B； UniProt 739–785	Mutation：residues 1-84 deleted, residues 223-440 replaced with GSGSGSGSGS, residues 606-738 deleted	WD repeat-containing protein 48 × 1 （Q8TAF3） ZN ZINC ION × 1 A1BWW 2-(4-cyclopropyl-6-methoxypyrimidin-5-yl)-7-({4-[1-methyl-4-(trifluoromethyl)-1H-imidazol-2-yl]phenyl}methyl)-5H-pyrrolo[3,2-d]pyrimidine × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；1M sodium citrate (pH 6.5)	Resolution 3.15 Å R-free 0.291

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 9N9Y	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7AY1 Cryo-EM structure of USP1-UAF1 bound to mono-ubiquitinated FANCD2, and FANCI Deposited 2020-11-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: heptameric	Chain D 1–785（785 aa）	Mutation：C90S, G670A, G671A	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å
7ZH3 USP1 bound to ubiquitin conjugated to FANCD2 (focused refinement) Deposited 2022-04-05	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1–785（785 aa）	Mutation：C90S	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；blotted for 3.0 secs before plunging	Resolution 2.50 Å
7ZH4 USP1 bound to ML323 and ubiquitin conjugated to FANCD2 (focused refinement) Deposited 2022-04-05	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1–785（785 aa）	Mutation：C90S	ZN ZINC ION × 1 JDA 5-methyl-2-(2-propan-2-ylphenyl)-~{N}-[[4-(1,2,3-triazol-1-yl)phenyl]methyl]pyrimidin-4-amine × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；blotting for 3.0 seconds	Resolution 2.49 Å
8A9J Cryo-EM structure of USP1-UAF1 bound to FANCI and mono-ubiquitinated FANCD2 without ML323 (consensus reconstruction) Deposited 2022-06-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: heptameric	Chain D 1–785（785 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；blotted for 3.0 secs before plunging	Resolution 2.80 Å
8A9K Cryo-EM structure of USP1-UAF1 bound to FANCI and mono-ubiquitinated FANCD2 with ML323 (consensus reconstruction) Deposited 2022-06-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: heptameric	Chain D 1–785（785 aa）	Not recorded	ZN ZINC ION × 1 JDA 5-methyl-2-(2-propan-2-ylphenyl)-~{N}-[[4-(1,2,3-triazol-1-yl)phenyl]methyl]pyrimidin-4-amine × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.85 Å
9DI1 Cryo-EM structure of the USP1-UAF1-Ubiquitin complex inhibited by KSQ-4279 Deposited 2024-09-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–785（785 aa）	Not recorded	ZN ZINC ION × 1 A1IB8 6-(4-cyclopropyl-6-methoxy-pyrimidin-5-yl)-1-[[4-[1-propan-2-yl-4-(trifluoromethyl)imidazol-2-yl]phenyl]methyl]pyrazolo[3,4-d]pyrimidine × 1 A1A4Y 3-(methanesulfonyl)propan-1-amine × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.70 Å
9DI2 Cryo-EM structure of the USP1-UAF1-Ubiquitin-VS complex Deposited 2024-09-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–785（785 aa）	Not recorded	ZN ZINC ION × 1 A1A4Y 3-(methanesulfonyl)propan-1-amine × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.60 Å
9EBS Cryo-EM structure of USP1-UAF1-Ubiquitin in complex with TNG348 Deposited 2024-11-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 1–785（785 aa）	Mutation：G670A,G671A	A1A4Y 3-(methanesulfonyl)propan-1-amine × 1 ZN ZINC ION × 1 A1BHF 2-(4-cyclopropyl-6-methoxypyrimidin-5-yl)-9-({4-[1-methyl-4-(trifluoromethyl)-1H-imidazol-2-yl]phenyl}methyl)-7-(2,2,2-trifluoroethyl)-7,9-dihydro-8H-purin-8-imine × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
9FCI USP1 bound to KSQ-4279 and ubiquitin conjugated to FANCD2 (focused refinement) Deposited 2024-05-15	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1–785（785 aa）	Mutation：C90S	ZN ZINC ION × 1 A1IB8 6-(4-cyclopropyl-6-methoxy-pyrimidin-5-yl)-1-[[4-[1-propan-2-yl-4-(trifluoromethyl)imidazol-2-yl]phenyl]methyl]pyrazolo[3,4-d]pyrimidine × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
9FCJ USP1 bound to ML323 and ubiquitin conjugated to FANCD2 (ordered subset, focused refinement) Deposited 2024-05-15	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1–785（785 aa）	Mutation：C90S	ZN ZINC ION × 1 JDA 5-methyl-2-(2-propan-2-ylphenyl)-~{N}-[[4-(1,2,3-triazol-1-yl)phenyl]methyl]pyrimidin-4-amine × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；blotting for 3.0 seconds	Resolution 2.70 Å
9HNW USP1-UAF1 bound to Lys63-linked diubiquitin Deposited 2024-12-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 21–785（765 aa）	Mutation：G670A, G671A	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.04 Å

11 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	UBP1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 2–139； UniProt 85–222 Author chain B； PDBConstruct 150–334； UniProt 421–605 Author chain B； PDBConstruct 335–381； UniProt 739–785

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	9n9y
Deposition date deposition_date	2025-02-11
Structure title title	Crystal structure of truncated USP1:UAF1 in complex with compound 18
Keywords keywords	ubiquitin, cysteine protease, allosteric inhibitor, HYDROLASE, HYDROLASE-INHIBITOR complex; HYDROLASE/INHIBITOR
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	35.38 Å
Radius of gyration Rg (electron density) rg_electron	35.17 Å
Forward intensity I(0) i0	276368000.00
Molecular weight molecular_weight	89008.0 kDa
Excluded volume excluded_volume	85859 Å³
Envelope volume envelope_volume	162310 Å³
Hydration-shell volume shell_volume	39005 Å³
Envelope diameter envelope_diameter	114.8 Å
Shell Rg shell_rg	40.92 Å
Envelope Rg envelope_rg	34.77 Å
Shape Rg shape_rg	35.18 Å
Total Rg total_rg	35.48 Å
Total atoms total_atoms	6729
Residues n_residues	844
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	112.2 Å
Rg (real space) rg_real	35.43 Å
Rg uncertainty (real space) rg_real_error	0.85 Å
I(0) (real space) i0_real	2.7640e+08
I(0) uncertainty (real space) i0_real_error	4.7240e+06
Rg (reciprocal space) rg_reciprocal	35.40 Å
I(0) (reciprocal space) i0_reciprocal	276400000.0000
Solution quality estimate total_estimate	0.6865
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	29.9 Å
Skewness Skewness skewness	0.253
Kurtosis Kurtosis kurtosis	-0.810
Angular range angular_range	— – 0.2250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	45880000.0000
Real-space data points n_real_points	46
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.869; Stabil: 1.000; Sysdev: 0.186; Positv: 1.000; Valcen: 0.930; Smooth: 0.823

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	WD repeat-containing protein 48
Molecular weight formula_weight	64019.4 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	6739

MAAHHRQNTAGRRKVQVSYVIRDEVEKYNRNGVNALQLDPALNRLFTAGRDSIIRIWSVNQHKQDPYIASMEHHTDWVNDIVLCCNGKTLISASSDTTVKVWNAHKGFCMSTLRTHKDYVKALAYAKDKELVASAGLDRQIFLWDVNTLTALTASNNTVTTSSLSGNKDSIYSLAMNQLGTIIVSGSTEKVLRVWDPRTCAKLMKLKGHTDNVKALLLNRDGTQCLSGSSDGTIRLWSLGQQRCIATYRVHDEGVWALQVNDAFTHVYSGGRDRKIYCTDLRNPDIRVLICEEKAPVLKMELDRSADPPPAIWVATTKSTVNKWTLKGIHNFRASGDYDNDCTNPITPLCTQPDQVIKGGASIIQCHILNDKRHILTKDTNNNVAYWDVLKACKVEDLGKVDFEDEIKKRFKMVYVPNWFSVDLKTGMLTITLDESDCFAAWVSAKDAGFSSPDGSDPKLNLGGLLLQALLEYWPRTHVNPMDEEENEVNHVNGEQENRVQKGNGYFQVPPHTPVIFGEAGGRTLFRLLCRDSGGETESMLLNETVPQWVIDITVDKNMPKFNENLYFQ

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	Trichoplusia ni

Entity 2 Entity 2 polymer

Description description	Ubiquitin carboxyl-terminal hydrolase 1, N-terminal fragment,Ubiquitin carboxyl-terminal hydrolase 1
Molecular weight formula_weight	42954.5 kDa
EC 编号 ec_number	3.4.19.12
Mutation mutation	residues 1-84 deleted, residues 223-440 replaced with GSGSGSGSGS, residues 606-738 deleted
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GNLGNTCYLNSILQVLYFCPGFKSGVKHLFNIISRKKEALKDEANQKDKGNCKEDSLASYELICSLQSLIISVEQLQASFLLNPEKYTDELATQPRRLLNTLRELNPMYEGYLQHDAQEVLQCILGNIQETCQLLKKEEGSGSGSGSGSIGFELVEKLFQGQLVLRTRCLECESLTERREDFQDISVPVQEDELSKVEESSEISPEPKTEMKTLRWAISQFASVERIVGEDKYFCENCHHYTEAERSLLFDKMPEVITIHLKCFAASGLEFDCYGGGLSKINTPLLTPLKLSLEEWSTKPTNDSYGLFAVVMHSGITISSGHYTASVKVTDLNSSLKEYEGKWLLFDDSEVKVTEEKDFLNSLSPSTSPTSTPYLLFYKKL

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	Trichoplusia ni

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	;2-(4-cyclopropyl-6-methoxypyrimidin-5-yl)-7-({4-[1-methyl-4-(trifluoromethyl)-1H-imidazol-2-yl]phenyl}methyl)-5H-pyrrolo[3,2-d]pyrimidine ;
Molecular weight formula_weight	505.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

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

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8. Citations (1)

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Unit-cell length a length_a	123.200 Å
Unit-cell length b length_b	161.880 Å
Unit-cell length c length_c	160.480 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	8

Space group space_group	I 2 2 2
Space-group number int_tables_number	23
Crystal system crystal_system	orthorhombic

Resolution resolution	3.150 Å
Low-resolution limit resolution_low	49.430 Å
R factor r_factor	0.2399
R_work r_work	0.2371
R_free r_free	0.2915

fit	/app/data/saxs_computation/n9/9n9y/9n9y.fit
pddf	/app/data/pr_computation/n9/9n9y/9n9y.pr.out
profile	/app/data/saxs_computation/n9/9n9y/9n9y.dat

Crystal structure of truncated USP1:UAF1 in complex with compound 18

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

WD repeat-containing protein 48

State in the Current Structure

Other States of the Same Protein in the Database

Ubiquitin carboxyl-terminal hydrolase 1, N-terminal fragment,Ubiquitin carboxyl-terminal hydrolase 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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)