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5hpt

System-wide modulation of HECT E3 ligases with selective ubiquitin variant probes: WWP1, Ubv P2.3 and UBCH7

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

NEDD4-like E3 ubiquitin-protein ligase WWP1

Homo sapiens

UniProt Q9H0M0

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 3 Ubiquitin variant P2.3 × 1 Ubiquitin-conjugating enzyme E2 L3 × 1 （P68036） water × 2 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 3 Ubiquitin variant P2.3 × 1 Ubiquitin-conjugating enzyme E2 L3 × 1 （P68036） water × 1 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 2 Ubiquitin variant P2.3 × 1 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
1nd7 2op7 6j1x 6j1y 6j1y 9eqk 9eqk

7 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
5hps 5hpt 5hpt 5hpt 8ei4

5 assemblies

View Construct and Data Evidence
UniProt name WWP1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 3–383； UniProt 537–917 Author chain D； PDBConstruct 3–383； UniProt 537–917 Author chain G； PDBConstruct 3–383； UniProt 537–917

Ubiquitin-conjugating enzyme E2 L3

Homo sapiens

UniProt P68036

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 3 NEDD4-like E3 ubiquitin-protein ligase WWP1 × 1 （Q9H0M0） Ubiquitin variant P2.3 × 1 water × 2 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 3 NEDD4-like E3 ubiquitin-protein ligase WWP1 × 1 （Q9H0M0） Ubiquitin variant P2.3 × 1 water × 1 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
6xxu

1 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1c4z 1fbv 3sqv 3sqv 3sqv 3sy2 3sy2 4q5e 4q5h 5hpt 5hpt 5tte

26 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name UB2L3_HUMAN
Isoform —
PDB entities 3
Chains and sequence ranges Author chain C； PDBConstruct 1–153； UniProt 2–154 Author chain F； PDBConstruct 1–153； UniProt 2–154

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_id5hpt
Deposition date deposition_date2016-01-20
Structure title titleSystem-wide modulation of HECT E3 ligases with selective ubiquitin variant probes: WWP1, Ubv P2.3 and UBCH7
Keywords keywordsHECT E3, WWP1, Ubiquitin, Ubv, UBCH7, LIGASE-TRANSFERASE complex; LIGASE/TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION
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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

5hpt__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

5hpt__assembly_1__model_1 | I(q)

10-2 10-1 106 107 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

5hpt__assembly_1__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）28.30 Å
Rg (electron density)27.26 Å
Total Rg28.08 Å
Atom count4952
Residues598
Excluded volume88719 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 5hpt__assembly_1__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 5hpt__assembly_2__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 5hpt__assembly_3__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (4)

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_idd5hpta_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.148 — Hect, E3 ligase catalytic domain
Superfamily Superfamily superfamilyd.148.1 — Hect, E3 ligase catalytic domain
Family Family familyd.148.1.0 — automated matches
Domain ID domain_idd5hptb_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamilyd.15.1 — Ubiquitin-like
Family Family familyd.15.1.0 — automated matches
Domain ID domain_idd5hptc_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.20 — UBC-like
Superfamily Superfamily superfamilyd.20.1 — UBC-like
Family Family familyd.20.1.0 — automated matches
Domain ID domain_idd5hptd_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.148 — Hect, E3 ligase catalytic domain
Superfamily Superfamily superfamilyd.148.1 — Hect, E3 ligase catalytic domain
Family Family familyd.148.1.0 — automated matches
Domain ID domain_idd5hpte_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamilyd.15.1 — Ubiquitin-like
Family Family familyd.15.1.0 — automated matches
Domain ID domain_idd5hptf_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.20 — UBC-like
Superfamily Superfamily superfamilyd.20.1 — UBC-like
Family Family familyd.20.1.0 — automated matches
Domain ID domain_idd5hptg_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.148 — Hect, E3 ligase catalytic domain
Superfamily Superfamily superfamilyd.148.1 — Hect, E3 ligase catalytic domain
Family Family familyd.148.1.0 — automated matches
Domain ID domain_idd5hpth_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamilyd.15.1 — Ubiquitin-like
Family Family familyd.15.1.0 — automated matches

CATH v4.4 (8 domains)

Domain ID domain_id5hptA01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology2160 — Hect, E3 ligase catalytic domain
Homologous superfamily homologous superfamily10 — Hect, E3 ligase catalytic domain
Domain ID domain_id5hptA02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology2410 — Hect, E3 ligase catalytic fold
Homologous superfamily homologous superfamily10 — Hect, E3 ligase catalytic domain
Domain ID domain_id5hptC00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology110 — Ubiquitin Conjugating Enzyme
Homologous superfamily homologous superfamily10 — Ubiquitin Conjugating Enzyme
Domain ID domain_id5hptD01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology2160 — Hect, E3 ligase catalytic domain
Homologous superfamily homologous superfamily10 — Hect, E3 ligase catalytic domain
Domain ID domain_id5hptD02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology2410 — Hect, E3 ligase catalytic fold
Homologous superfamily homologous superfamily10 — Hect, E3 ligase catalytic domain
Domain ID domain_id5hptF00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology110 — Ubiquitin Conjugating Enzyme
Homologous superfamily homologous superfamily10 — Ubiquitin Conjugating Enzyme
Domain ID domain_id5hptG01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology2160 — Hect, E3 ligase catalytic domain
Homologous superfamily homologous superfamily10 — Hect, E3 ligase catalytic domain
Domain ID domain_id5hptG02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology2410 — Hect, E3 ligase catalytic fold
Homologous superfamily homologous superfamily10 — Hect, E3 ligase catalytic domain
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7. Citations (1)