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Protein Structures and Oligomeric States

Enter a protein name, UniProt accession or PDB ID. Name searches ask you to confirm the protein identity before related structures are queried.

Current Protein Identity：Q96PU5 New Search
19PDB entries
26Biological assembly
31chain/assembly records
Main Difference Dimensions in This Set
Different construct Different mutation/modification Different assembly state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics

Difference tags compare only the current result set; every original PDB and assembly record remains separate.

Related-Structure Differences

Each row represents one biological assembly in one PDB entry; multiple monomers of the same protein are listed separately.

PDB Entry Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Experimental Method Experimental Conditions Structure Quality
2LAJ Third WW domain of human Nedd4L in complex with doubly phosphorylated human smad3 derived peptide Deposited 2011-03-16 Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain A 496–535（40 aa） Fragment：WW 3 domain residues 496-535
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；285 K；Ionic strength (raw mmCIF value) 0.420；Pressure ambient
NMR sample composition 1 mM NEDD4LWW3, 3 mM SMAD3, 20 mM sodium phosphate, 100 mM sodium chloride, 2 mM sodium azide, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1 mM [U-100% 15N] NEDD4LWW3, 3 mM SMAD3, 20 mM sodium phosphate, 100 mM sodium chloride, 2 mM sodium azide, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1 mM [U-100% 13C; U-100% 15N] NEDD4LWW3, 3 mM SMAD3, 20 mM sodium phosphate, 100 mM sodium chloride, 2 mM sodium azide, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2LB2 Structure of the second domain of human Nedd4L in complex with a phosphorylated pTPY motif derived from human Smad3 Deposited 2011-03-22 Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain A 386–420（35 aa） Fragment：residues 386-420
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；285 K；Ionic strength (raw mmCIF value) 0.420；Pressure ambient
NMR sample composition 1 mM NEDD4LWW3, 3 mM SMAD3, 20 mM sodium phosphate, 100 mM sodium chloride, 2 mM sodium azide, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1 mM [U-100% 15N] NEDD4LWW3, 3 mM SMAD3, 20 mM sodium phosphate, 100 mM sodium chloride, 2 mM sodium azide, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1 mM [U-100% 13C; U-100% 15N] NEDD4LWW3, 3 mM SMAD3, 20 mM sodium phosphate, 100 mM sodium chloride, 2 mM sodium azide, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2LTY NEDD4L WW2 domain in complex with a Smad7 derived peptide Deposited 2012-06-04 Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain A 385–417（33 aa） Fragment：WW2 domain (UNP residues 385-417)
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.2；285 K；Pressure ambient
NMR sample composition 1 mM NEDD4LWW2, 2 mM SMAD7, 20 mM [U-100% 2H] TRIS, 100 mM sodium chloride, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1 mM [U-100% 13C; U-100% 15N] NEDD4LWW2, 3 mM SMAD7, 20 mM [U-100% 2H] TRIS, 100 mM sodium chloride, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2MPT WW3 domain of Nedd4L in complex with its HECT domain PY motif Deposited 2014-06-02 Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain A 496–539（44 aa） Fragment：WW3 domain, UNP RESIDUES 496-539
Chain B 945–957（13 aa） Fragment：HECT domain PY motif, UNP RESIDUES 945-957
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；298 K；Pressure ambient
NMR sample composition 0.7 mM WW3-1, 1.4 mM HECT_PY-2, 150 mM sodium chloride-3, 20 mM sodium phosphate-4, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1 mM [U-100% 15N] WW3-5, 2 mM HECT_PY-6, 150 mM sodium chloride-7, 20 mM sodium phosphate-8, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.8 mM [U-100% 13C; U-100% 15N] WW3-9, 1.6 mM HECT_PY-10, 150 mM sodium chloride-11, 20 mM sodium phosphate-12, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2NSQ Crystal structure of the C2 domain of the human E3 ubiquitin-protein ligase NEDD4-like protein Deposited 2006-11-06 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 1–154（154 aa） Fragment：C2 Domain
Not recorded EDO 1,2-ETHANEDIOL × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；298 K；14% PEG 4000, 0.2 M NaOAc, pH 6.5, 1 mM DTT. 20% Ethylene glycol added as cryoprotectant, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K, pH 6.50
Resolution 1.85 Å R-free 0.218
2ONI Catalytic Domain of the Human NEDD4-like E3 Ligase Deposited 2007-01-24 Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain A 594–967（374 aa） Fragment：Hect Domain (ubiquitin transferase)
Non-standard monomer：Yes (specific site not provided by mmCIF) NA SODIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；294 K；THE PROTEIN WAS DISSOLVED AT 10 mg/mL IN 10 mM TRIS-HCL, PH 8.0, 100 mM NaCl, 2% GLYCEROL AND 1 mM DTT. CRYSTALS WERE GROWN BY VAPOR DIFFUSION, HANGING DROPS BY MIXING 2 MICROL PROTEIN SOLUTION WITH 2 MICROL WELL SOLUTION (1.7 M SODIUM/POTASSIUM PHOSPHATE, PH 6.0, 1 mM DTT) AT TEMPERATURE 294.0K. FOR CRYOPROTECTION, THE CRYSTALS WERE SOAKED IN 2 M SODIUM-POTASSIUM PHOSPHATE, pH 7.0, 1 mM DTT, 25% ETHYLENE GLYCOL AND 2 mG/mL SEMETNEDD4L.574.947.
Resolution 2.20 Å R-free 0.259
2ONI Catalytic Domain of the Human NEDD4-like E3 Ligase Deposited 2007-01-24 Assembly 2 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count
Chain A 594–967（374 aa） Fragment：Hect Domain (ubiquitin transferase)
Non-standard monomer：Yes (specific site not provided by mmCIF) NA SODIUM ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；294 K；THE PROTEIN WAS DISSOLVED AT 10 mg/mL IN 10 mM TRIS-HCL, PH 8.0, 100 mM NaCl, 2% GLYCEROL AND 1 mM DTT. CRYSTALS WERE GROWN BY VAPOR DIFFUSION, HANGING DROPS BY MIXING 2 MICROL PROTEIN SOLUTION WITH 2 MICROL WELL SOLUTION (1.7 M SODIUM/POTASSIUM PHOSPHATE, PH 6.0, 1 mM DTT) AT TEMPERATURE 294.0K. FOR CRYOPROTECTION, THE CRYSTALS WERE SOAKED IN 2 M SODIUM-POTASSIUM PHOSPHATE, pH 7.0, 1 mM DTT, 25% ETHYLENE GLYCOL AND 2 mG/mL SEMETNEDD4L.574.947.
Resolution 2.20 Å R-free 0.259
2ONI Catalytic Domain of the Human NEDD4-like E3 Ligase Deposited 2007-01-24 Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 594–967（374 aa） Fragment：Hect Domain (ubiquitin transferase)
Non-standard monomer：Yes (specific site not provided by mmCIF) NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；294 K；THE PROTEIN WAS DISSOLVED AT 10 mg/mL IN 10 mM TRIS-HCL, PH 8.0, 100 mM NaCl, 2% GLYCEROL AND 1 mM DTT. CRYSTALS WERE GROWN BY VAPOR DIFFUSION, HANGING DROPS BY MIXING 2 MICROL PROTEIN SOLUTION WITH 2 MICROL WELL SOLUTION (1.7 M SODIUM/POTASSIUM PHOSPHATE, PH 6.0, 1 mM DTT) AT TEMPERATURE 294.0K. FOR CRYOPROTECTION, THE CRYSTALS WERE SOAKED IN 2 M SODIUM-POTASSIUM PHOSPHATE, pH 7.0, 1 mM DTT, 25% ETHYLENE GLYCOL AND 2 mG/mL SEMETNEDD4L.574.947.
Resolution 2.20 Å R-free 0.259
3JVZ E2~Ubiquitin-HECT Deposited 2009-09-17 Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain C 596–975（380 aa） Fragment：HECT domain
Mutation：576-949, C922A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.1；277 K；0.1 M sodium citrate, pH 5.1-5.2, 2.4-2.5 M sodium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.30 Å R-free 0.267
3JVZ E2~Ubiquitin-HECT Deposited 2009-09-17 Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain D 596–975（380 aa） Fragment：HECT domain
Mutation：576-949, C922A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.1；277 K；0.1 M sodium citrate, pH 5.1-5.2, 2.4-2.5 M sodium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.30 Å R-free 0.267
3JW0 E2~Ubiquitin-HECT Deposited 2009-09-17 Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain C 596–975（380 aa） Fragment：NEDD4L HECT DOMAIN (UNP 576-955)
Mutation：UBIQUITIN G76 ESTER-LINKED TO UBCH5B TO S85 No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.1；277 K；0.1 M sodium citrate, 2.4M sodium chloride, pH 5.1, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.10 Å R-free 0.287
3JW0 E2~Ubiquitin-HECT Deposited 2009-09-17 Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain D 596–975（380 aa） Fragment：NEDD4L HECT DOMAIN (UNP 576-955)
Mutation：UBIQUITIN G76 ESTER-LINKED TO UBCH5B TO S85 No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.1；277 K；0.1 M sodium citrate, 2.4M sodium chloride, pH 5.1, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.10 Å R-free 0.287
5HPK System-wide modulation of HECT E3 ligases with selective ubiquitin variant probes: NEDD4L and UbV NL.1 Deposited 2016-01-20 Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain A 594–975（382 aa） Fragment：HECT domain (UNP residues 594-975)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；Sodium cacodylate, NaCl, PEG 8000, 1-butanol
Resolution 2.43 Å R-free 0.227
6ZBT Structure of 14-3-3 gamma in complex with Nedd4-2 14-3-3 binding motif Ser342 Deposited 2020-06-09 Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
Chain E 338–347（10 aa）
Chain G 338–347（10 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) CFH 1,1,1,3,3,3-hexafluoropropan-2-ol × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293.15 K；PEG 400, magnesium chloride, HEPES, hexafluoro-2-propanol
Resolution 1.80 Å R-free 0.241
6ZBT Structure of 14-3-3 gamma in complex with Nedd4-2 14-3-3 binding motif Ser342 Deposited 2020-06-09 Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
Chain F 338–347（10 aa）
Chain H 338–347（10 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) CFH 1,1,1,3,3,3-hexafluoropropan-2-ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293.15 K；PEG 400, magnesium chloride, HEPES, hexafluoro-2-propanol
Resolution 1.80 Å R-free 0.241
6ZC9 Structure of 14-3-3 gamma in complex with Nedd4-2 14-3-3 binding motif Ser448 Deposited 2020-06-10 Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
Chain E 444–453（10 aa）
Chain G 444–453（10 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293.15 K；PEG 400, magnesium chloride, HEPES, hexafluoro-2-propanol
Resolution 1.90 Å R-free 0.239
6ZC9 Structure of 14-3-3 gamma in complex with Nedd4-2 14-3-3 binding motif Ser448 Deposited 2020-06-10 Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
Chain F 444–453（10 aa）
Chain H 444–453（10 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) CFH 1,1,1,3,3,3-hexafluoropropan-2-ol × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293.15 K；PEG 400, magnesium chloride, HEPES, hexafluoro-2-propanol
Resolution 1.90 Å R-free 0.239
7LP1 Structure of Nedd4L WW3 domain Deposited 2021-02-11 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 494–532（39 aa） Fragment：WW 3 domain, residues 494-532
Not recorded NO3 NITRATE ION × 3 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；293.15 K；3.6M ammonium nitrate, 5% glycerol, and 0.1M sodium acetate at pH 4.6
Resolution 1.35 Å R-free 0.213
7LP3 Structure of Nedd4L WW3 domain Deposited 2021-02-11 Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain A 193–226（34 aa） Fragment：WW 1 domain, residues 193-226
Not recorded SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；310 K；1.6M (NH4)2SO4, 0.1M Potassium Sodium Tartrate, 5% glycerol, 0.1M Sodium Acetate
Resolution 1.61 Å R-free 0.210
7LP3 Structure of Nedd4L WW3 domain Deposited 2021-02-11 Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain C 193–226（34 aa） Fragment：WW 1 domain, residues 193-226
Not recorded SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；310 K；1.6M (NH4)2SO4, 0.1M Potassium Sodium Tartrate, 5% glycerol, 0.1M Sodium Acetate
Resolution 1.61 Å R-free 0.210
7LP4 Structure of Nedd4L WW3 domain Deposited 2021-02-11 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 493–539（47 aa） Fragment：WW 3 domain, residues 493-539
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.5；298 K；Ionic strength (raw mmCIF value) 50；Pressure 1
NMR sample composition 1 mM [U-100% 13C; U-100% 15N] E3 ubiquitin-protein ligase NEDD4-like, 20 mM sodium phosphate, 50 mM sodium chloride, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1 mM [U-100% 15N] E3 ubiquitin-protein ligase NEDD4-like, 20 mM sodium phosphate, 50 mM sodium chloride, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
7LP5 Structure of Nedd4L WW3 domain Deposited 2021-02-11 Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 493–539（47 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.5；298 K；Ionic strength (raw mmCIF value) 50；Pressure 1
NMR sample composition 1 mM [U-100% 13C; U-100% 15N] Angiomotin,E3 ubiquitin-protein ligase NEDD4-like fusion, 20 mM sodium phosphate, 50 mM sodium chloride, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1 mM [U-100% 15N] Angiomotin,E3 ubiquitin-protein ligase NEDD4-like fusion, 20 mM sodium phosphate, 50 mM sodium chloride, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
7NMZ Structure of 14-3-3 eta in complex with Nedd4-2(335-455) containing two 14-3-3 binding motifs Ser342 and Ser448 Deposited 2021-02-23 Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain C 335–455（121 aa）
Mutation：T367A Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293.15 K；12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 0.03M of each NPS (sodium nitrate, sodium phosphate dibasic, ammonium sulfate), 0.1Mbicine/Trizma base pH 8.5, 30% sacharose
Resolution 2.30 Å R-free 0.235
9GIK Full-lenght Nedd4-2 E3 ubiquitin ligase Deposited 2024-08-19 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 1–955（955 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES pH 7.5, 130 mM KCl, 20 mM NaCl, 1 mM EDTA, 1 mM TCEP, 3mM CHAPSO
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.58 Å
9GIM Full-lenght Nedd4-2 E3 ubiquitin ligase in presence of Ca2+ Deposited 2024-08-19 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 1–955（955 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES pH 7.5, 130 mM KCl, 20 mM NaCl, 1 mM TCEP, 1mM CaCl2, 3mM CHAPSO
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.11 Å
9Z5Q HECT domain of NEDD4-2 complex with a targeted nanobody, nb.C11 Deposited 2025-11-12 Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain B 541–975（435 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES pH 7.5, 150 mM NaCl, 1 mM TCEP, and 1 mM EDTA, 0.043% CHAPS
cryo-EM vitrification conditions Cryogen ETHANE；Vitrification carried out at Argon atmosphere
Resolution 3.06 Å

This page presents structural evidence recorded in PDB/mmCIF.“No recorded non-water small molecule” does not prove that the experimental sample was ligand-free; experimental conditions belong to the PDB experiment, while ligands and copy counts are shown for each biological assembly.