Current Protein Identity：P46934
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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 |
|---|---|---|---|---|---|---|---|
| 2KPZ Human NEDD4 3RD WW Domain Complex with The Human T-cell Leukemia virus 1 GAG-Pro poliprotein Derived Peptide SDPQIPPPYVEP Deposited 2009-10-23 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain A
834–878（45 aa）
Fragment：3rd WW Domain, UNP residues 834-878
|
Not recorded | No recorded non-water small molecule | SOLUTION NMR |
NMR measurement conditions
pH 7；288 K；Pressure ambient
NMR sample composition
1 mM [U-100% 15N] PROTEIN-1; 3 mM PEPTIDE-2; 20 mM sodium phosphate-3; 0.02 v/v sodium azide-4; 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition
1 mM [U-100% 13C; U-100% 15N] PROTEIN-5; 3 mM PEPTIDE-6; 20 mM sodium phosphate-7; 0.02 v/v sodium azide-8; 90% H2O/10% D2O | 90% H2O/10% D2O
|
Resolution not provided |
| 2KQ0 Human NEDD4 3rd WW Domain Complex with Ebola Zaire Virus Matrix Protein VP40 Derived Peptide ILPTAPPEYMEA Deposited 2009-10-23 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain A
834–878（45 aa）
Fragment：3rd WW Domain, UNP residues 834-878
|
Not recorded | No recorded non-water small molecule | SOLUTION NMR |
NMR measurement conditions
pH 7；288 K；Pressure ambient
NMR sample composition
1mM [U-100% 15N] PROTEIN; 10mM PEPTIDE; 20mM sodium phosphate; 0.02 v/v % sodium azide; 90% H2O/10% D2O | 90% H2O/10% D2O
|
Resolution not provided |
| 2M3O Structure and dynamics of a human Nedd4 WW domain-ENaC complex Deposited 2013-01-23 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain W
838–877（40 aa）
Fragment：third WW domain
|
Not recorded | No recorded non-water small molecule | SOLUTION NMR |
NMR measurement conditions
pH 6.5；298 K；Ionic strength (raw mmCIF value) 0.02；Pressure ambient
NMR sample composition
1.1 mM [U-99% 13C; U-99% 15N] Nedd4 WW3* domain, 2.2 mM alpha ENaC PY peptide, 20 mM sodium phosphate, 0.1 % sodium azide, 1 mM TSP, 93% H2O/7% D2O | 93% H2O/7% D2O
NMR sample composition
3.0 mM Nedd4 WW3* domain, 1.5 mM [U-99% 13C; U-99% 15N] alpha ENaC PY peptide, 20 mM sodium phosphate, 0.1 % sodium azide, 1.0 mM TSP, 93% H2O/7% D2O | 93% H2O/7% D2O
NMR sample composition
1.61 mM [U-99% 15N] Nedd4 WW3* domain, 4.38 mM alpha ENaC PY peptide, 20 mM sodium phosphate, 0.1 % sodium azide, 1 mM TSP, 93% H2O/7% D2O | 93% H2O/7% D2O
|
Resolution not provided |
| 2XBB Nedd4 HECT:Ub complex Deposited 2010-04-08 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain A
519–900（382 aa）
Fragment：HECT DOMAIN, RESIDUES 519-900
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
pH 7.5；100 MM NA-HEPES, PH 7.5, 10% PEG 2000 MME, 5 MM TCEP.
|
Resolution 2.68 Å R-free 0.249 |
| 2XBB Nedd4 HECT:Ub complex Deposited 2010-04-08 | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
519–900（382 aa）
Fragment：HECT DOMAIN, RESIDUES 519-900
|
Not recorded | GOL GLYCEROL × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
pH 7.5；100 MM NA-HEPES, PH 7.5, 10% PEG 2000 MME, 5 MM TCEP.
|
Resolution 2.68 Å R-free 0.249 |
| 2XBF Nedd4 HECT structure Deposited 2010-04-09 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
519–900（382 aa）
Fragment：HECT DOMAIN, RESIDUES 519-900
|
Not recorded | EDO 1,2-ETHANEDIOL × 4 CA CALCIUM ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
pH 6；100 MM NA-MES, PH 6.0, 4% PEG 400, 35 MM CACL2, 5 MM TCEP
|
Resolution 2.50 Å R-free 0.256 |
| 3B7Y Crystal structure of the C2 Domain of the E3 Ubiquitin-Protein Ligase NEDD4 Deposited 2007-10-31 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
101–252（152 aa）
Fragment：C2 Domain: Residues 101-252
|
Not recorded | CA CALCIUM ION × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；10% PEG 4000, 0.1 M Succinic acid pH 7.0, 0.01M Spermine tetra-HCl, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
|
Resolution 1.80 Å R-free 0.209 |
| 3B7Y Crystal structure of the C2 Domain of the E3 Ubiquitin-Protein Ligase NEDD4 Deposited 2007-10-31 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain B
101–252（152 aa）
Fragment：C2 Domain: Residues 101-252
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；10% PEG 4000, 0.1 M Succinic acid pH 7.0, 0.01M Spermine tetra-HCl, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
|
Resolution 1.80 Å R-free 0.209 |
| 4BBN NEDD4 HECT-Ub:Ub complex Deposited 2012-09-27 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain A
892–1318（427 aa）
Fragment：HECT DOMAIN, RESIDUES 892-1318
|
Mutation：YES | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
pH 6；2.5 SODIUM MALONATE, PH 6.0
|
Resolution 2.51 Å R-free 0.224 |
| 4BE8 NEDD4 HECT A889F structure Deposited 2013-03-06 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
519–900（382 aa）
Fragment：HECT DOMAIN, RESIDUES 519-900
|
Mutation：YES | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
pH 9；1.15 M POTASSIUM SODIUM TARTRATE, 0.1 M TRIS-HCL, PH 9.0
|
Resolution 3.00 Å R-free 0.295 |
| 4N7F Crystal structure of 3rd WW domain of human Nedd4-1 Deposited 2013-10-15 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
841–874（34 aa）
Fragment：WW3 domain (UNP residues 841-874)
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；294 K；3.0M NaCl, 100mM Tris-HCl 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K
|
Resolution 1.10 Å R-free 0.200 |
| 4N7F Crystal structure of 3rd WW domain of human Nedd4-1 Deposited 2013-10-15 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain B
841–874（34 aa）
Fragment：WW3 domain (UNP residues 841-874)
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；294 K；3.0M NaCl, 100mM Tris-HCl 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K
|
Resolution 1.10 Å R-free 0.200 |
| 4N7H Crystal Structure of the Complex of 3rd WW domain of Human Nedd4 and 1st PPXY Motif of ARRDC3 Deposited 2013-10-15 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain A
840–872（33 aa）
Fragment：3rd WW domain (UNP residues 840-872)
|
Not recorded | GAI GUANIDINE × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；294 K；0.35M (NH4)SO4, 100mM Tris-HCl 8.0, 100mM Guanidine-HCl, VAPOR DIFFUSION, HANGING DROP, temperature 294K
|
Resolution 1.70 Å R-free 0.233 |
| 5AHT Third WW domain from the E3 ubiquitin-protein ligase NEDD4 Deposited 2015-02-09 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
838–877（40 aa）
Fragment：WW3, UNP RESIDUES 838-877
|
Not recorded | No recorded non-water small molecule | SOLUTION NMR |
NMR measurement conditions
pH 6.5；298 K；Ionic strength (raw mmCIF value) 0.05；Pressure 1.0
NMR sample composition
1.5 MM [U-99% 13C
NMR sample composition
U-99% 15N] NEDD4 WW3* DOMAIN, 20 MM SODIUM PHOSPHATE, 50 MM SODIUM CHLORIDE, 0.5 MM DSS, 90% 2O/10% D2O
|
Resolution not provided |
| 5C7J CRYSTAL STRUCTURE OF NEDD4 WITH A UB VARIANT Deposited 2015-06-24 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain A
520–900（381 aa）
Fragment：HECT DOMAIN (UNP RESIDUES 520-900)
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；The NEDD4 and Ubiquitin Variant was mixed at molar ratio ~1:2, and then concentrated to 15mg/ml.
The protein sample was mixed with Trypsin at a 1:1000 (W/W) Trypsin:protein ratio before setting up crystallization.
Crystal was initially obtained from Molecular Dimentions Proplex screen condition E04.
Crystal used for structure refinement was grown in 20% PEG8000, 10% Glycerol, 0.1M HEPES pH 7.0 in hanging drop setup, using 1.5uL protein, 1.5uL well solution over 0.5 mL reservoir buffer at 20 C.
Crystals grow to mountable size in 4 days. Harvested crystal was flash-frozen in liquid nitrogen. 20% Glycerol was used as the cryo-protectant
|
Resolution 3.00 Å R-free 0.277 |
| 5C7J CRYSTAL STRUCTURE OF NEDD4 WITH A UB VARIANT Deposited 2015-06-24 | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
520–900（381 aa）
Fragment：HECT DOMAIN (UNP RESIDUES 520-900)
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；The NEDD4 and Ubiquitin Variant was mixed at molar ratio ~1:2, and then concentrated to 15mg/ml.
The protein sample was mixed with Trypsin at a 1:1000 (W/W) Trypsin:protein ratio before setting up crystallization.
Crystal was initially obtained from Molecular Dimentions Proplex screen condition E04.
Crystal used for structure refinement was grown in 20% PEG8000, 10% Glycerol, 0.1M HEPES pH 7.0 in hanging drop setup, using 1.5uL protein, 1.5uL well solution over 0.5 mL reservoir buffer at 20 C.
Crystals grow to mountable size in 4 days. Harvested crystal was flash-frozen in liquid nitrogen. 20% Glycerol was used as the cryo-protectant
|
Resolution 3.00 Å R-free 0.277 |
| 5C91 NEDD4 HECT with covalently bound indole-based inhibitor Deposited 2015-06-26 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
938–1312（375 aa）
Fragment：unp residues 938-1312
|
Not recorded | 4YU methyl (2E)-4-{[(5-methoxy-1,2-dimethyl-1H-indol-3-yl)carbonyl]amino}but-2-enoate × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；100 mM MES, 35 mM calcium chloride, 5 mM TCEP, 6% PEG400
|
Resolution 2.44 Å R-free 0.298 |
| 9H9O Crystal structure of NEDD4 HECT domain in complex with norclomipramine Deposited 2024-10-31 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
519–893（375 aa）
|
Not recorded | EDO 1,2-ETHANEDIOL × 4 A1ITH Norclomipramine × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；100 mM MES pH 6.0
8-10% PEG 400
20% glycerol
1-4 mM inhibitor (0.25-1% DMSO)
|
Resolution 2.12 Å R-free 0.236 |
| 9H9T Crystal structure of NEDD4 HECT domain in complex with covalent inhibitor Deposited 2024-10-31 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
519–893（375 aa）
|
Not recorded | A1ITT ethyl 4-[4-(2-chloranyl-5,6-dihydrobenzo[b][1]benzazepin-11-yl)butylamino]butanoate × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；100 mM MES pH 6.0
8-10% PEG 400
20% glycerol
1-4 mM inhibitor (0.25-1% DMSO)
|
Resolution 2.17 Å R-free 0.252 |