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5k1a

Crystal structure of the UAF1-USP12 complex in C2 space group

Method: X-RAY DIFFRACTION Dmax: 209.3 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Ubiquitin carboxyl-terminal hydrolase 12

Homo sapiens

UniProt O75317

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 40–370 Fragment：residues 40-370 WD repeat-containing protein 48 × 1 （Q8TAF3） 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
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain C； UniProt 40–370 Fragment：residues 40-370 WD repeat-containing protein 48 × 1 （Q8TAF3） 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
3 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain E； UniProt 40–370 Fragment：residues 40-370 WD repeat-containing protein 48 × 1 （Q8TAF3） 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
4 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain G； UniProt 40–370 Fragment：residues 40-370 WD repeat-containing protein 48 × 1 （Q8TAF3） 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

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 5K1A Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5K16 Crystal structure of free Ubiquitin-specific protease 12 Deposited 2016-05-17 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 16–370（355 aa） Fragment：residues 16-370
Not recorded ZN ZINC ION × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；0.1 M Tris-HCl, 18% PEG 3350, 0.2 M Lithium Sulfate
Resolution 2.60 Å R-free 0.246
5K16 Crystal structure of free Ubiquitin-specific protease 12 Deposited 2016-05-17 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 16–370（355 aa） Fragment：residues 16-370
Not recorded ZN ZINC ION × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；0.1 M Tris-HCl, 18% PEG 3350, 0.2 M Lithium Sulfate
Resolution 2.60 Å R-free 0.246
5K16 Crystal structure of free Ubiquitin-specific protease 12 Deposited 2016-05-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 16–370（355 aa） Fragment：residues 16-370
Chain B 16–370（355 aa） Fragment：residues 16-370
Not recorded ZN ZINC ION × 2 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；0.1 M Tris-HCl, 18% PEG 3350, 0.2 M Lithium Sulfate
Resolution 2.60 Å R-free 0.246
5K1B Crystal structure of the UAF1/USP12 complex in F222 space group Deposited 2016-05-18 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 4–370（367 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 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 16–370（355 aa） Fragment：residues 16-370
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
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 A 1–370（370 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

4 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name UBP12_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–331； UniProt 40–370 Author chain C； PDBConstruct 1–331； UniProt 40–370 Author chain E； PDBConstruct 1–331； UniProt 40–370 Author chain G； PDBConstruct 1–331； UniProt 40–370

WD repeat-containing protein 48

Homo sapiens

UniProt Q8TAF3

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 1–677 Not recorded Ubiquitin carboxyl-terminal hydrolase 12 × 1 （O75317） 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
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain D； UniProt 1–677 Not recorded Ubiquitin carboxyl-terminal hydrolase 12 × 1 （O75317） 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
3 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain F； UniProt 1–677 Not recorded Ubiquitin carboxyl-terminal hydrolase 12 × 1 （O75317） 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
4 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain H； UniProt 1–677 Not recorded Ubiquitin carboxyl-terminal hydrolase 12 × 1 （O75317） 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

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 5K1A 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 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 oligomeric state 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 oligomeric state 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
5K1B Crystal structure of the UAF1/USP12 complex in F222 space group Deposited 2016-05-18 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 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 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 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 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 oligomeric state 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 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 oligomeric state 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 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 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 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 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 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
9N9Y Crystal structure of truncated USP1:UAF1 in complex with compound 18 Deposited 2025-02-11 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） Fragment：residues 1-563
Not recorded 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

18 other PDB entries and 22 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name WDR48_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–677； UniProt 1–677 Author chain D； PDBConstruct 1–677； UniProt 1–677 Author chain F； PDBConstruct 1–677； UniProt 1–677 Author chain H； PDBConstruct 1–677； UniProt 1–677

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

SAXS profile for 5k1a

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5k1a
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5k1a
Deposition date deposition_date2016-05-18
Structure title titleCrystal structure of the UAF1-USP12 complex in C2 space group
Keywords keywords;WD40 domain, Ubiquitin-specific protease 12, USP12, USP1-associated factor 1, USP1, Deubiquitinating enzyme, DUB, SUMO-like domain, SLD, HYDROLASE ;; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier61.58 Å
Radius of gyration Rg (electron density) rg_electron61.89 Å
Forward intensity I(0) i01917320000.00
Molecular weight molecular_weight370950.0 kDa
Excluded volume excluded_volume465380 ų
Envelope volume envelope_volume729910 ų
Hydration-shell volume shell_volume100400 ų
Envelope diameter envelope_diameter202.6 Å
Shell Rg shell_rg61.22 Å
Envelope Rg envelope_rg59.30 Å
Shape Rg shape_rg61.89 Å
Total Rg total_rg61.87 Å
Total atoms total_atoms26064
Residues n_residues3307
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax209.3 Å
Rg (real space) rg_real61.79 Å
Rg uncertainty (real space) rg_real_error1.69 Å
I(0) (real space) i0_real1.9170e+09
I(0) uncertainty (real space) i0_real_error3.7570e+07
Rg (reciprocal space) rg_reciprocal61.36 Å
I(0) (reciprocal space) i0_reciprocal1916000000.0000
Solution quality estimate total_estimate0.7881
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary58.6 Å
Skewness Skewness skewness0.327
Kurtosis Kurtosis kurtosis-0.661
Angular range angular_range— – 0.1250 Å−1
Current regularization parameter α current_alpha0.0025
Highest regularization parameter α highest_alpha90200000.0000
Real-space data points n_real_points26
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.747; Stabil: 1.000; Sysdev: 1.000; 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 (4)

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8. Citations (1)

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9. Files and Curves (10)