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8fy2

E3:PROTAC:target ternary complex structure (VCB/WH244/BCL-2)

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

von Hippel-Lindau disease tumor suppressor

Homo sapiens

UniProt P40337

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 4 Elongin-B × 1 （Q15370） Elongin-C × 1 （Q15369） Apoptosis regulator Bcl-2 × 1 （P10415） ;N-({4-[2-(4-{[(4R)-4'-chloro-4-methyl-6-{[4-(4-{[4-{[(2R)-4-[(1R,4R)-2-oxa-5-azabicyclo[2.2.1]heptan-5-yl]-1-(phenylsulfanyl)butan-2-yl]amino}-3-(trifluoromethanesulfonyl)benzene-1-sulfonyl]carbamoyl}phenyl)piperazin-1-yl]methyl}-2,3,4,5-tetrahydro[1,1'-biphenyl]-4-yl]methyl}piperazin-1-yl)-2-oxoethyl]piperazin-1-yl}acetyl)-3-methyl-L-valyl-(4S)-4-hydroxy-N-{(1S)-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl}-L-prolinamide ; × 1 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1lm8 1lqb 1lqb 1vcb 1vcb 1vcb 1vcb 3zrc 3zrc 3zrc 3zrc 3zrf

364 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name VHL_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 21–180； UniProt 54–213

Elongin-B

Homo sapiens

UniProt Q15370

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 4 von Hippel-Lindau disease tumor suppressor × 1 （P40337） Elongin-C × 1 （Q15369） Apoptosis regulator Bcl-2 × 1 （P10415） ;N-({4-[2-(4-{[(4R)-4'-chloro-4-methyl-6-{[4-(4-{[4-{[(2R)-4-[(1R,4R)-2-oxa-5-azabicyclo[2.2.1]heptan-5-yl]-1-(phenylsulfanyl)butan-2-yl]amino}-3-(trifluoromethanesulfonyl)benzene-1-sulfonyl]carbamoyl}phenyl)piperazin-1-yl]methyl}-2,3,4,5-tetrahydro[1,1'-biphenyl]-4-yl]methyl}piperazin-1-yl)-2-oxoethyl]piperazin-1-yl}acetyl)-3-methyl-L-valyl-(4S)-4-hydroxy-N-{(1S)-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl}-L-prolinamide ; × 1 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1lm8 1lqb 1lqb 1vcb 1vcb 1vcb 1vcb 2c9w 2izv 2jz3 2ma9 3dcg

479 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name ELOB_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–118； UniProt 1–118

Elongin-C

Homo sapiens

UniProt Q15369

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 4 von Hippel-Lindau disease tumor suppressor × 1 （P40337） Elongin-B × 1 （Q15370） Apoptosis regulator Bcl-2 × 1 （P10415） ;N-({4-[2-(4-{[(4R)-4'-chloro-4-methyl-6-{[4-(4-{[4-{[(2R)-4-[(1R,4R)-2-oxa-5-azabicyclo[2.2.1]heptan-5-yl]-1-(phenylsulfanyl)butan-2-yl]amino}-3-(trifluoromethanesulfonyl)benzene-1-sulfonyl]carbamoyl}phenyl)piperazin-1-yl]methyl}-2,3,4,5-tetrahydro[1,1'-biphenyl]-4-yl]methyl}piperazin-1-yl)-2-oxoethyl]piperazin-1-yl}acetyl)-3-methyl-L-valyl-(4S)-4-hydroxy-N-{(1S)-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl}-L-prolinamide ; × 1 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1lm8 1lqb 1lqb 1vcb 1vcb 1vcb 1vcb 2c9w 2izv 2ma9 3dcg 3dcg

468 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name ELOC_HUMAN
Isoform —
PDB entities 3
Chains and sequence ranges Author chain C； PDBConstruct 1–96； UniProt 17–112

Apoptosis regulator Bcl-2

Homo sapiens

UniProt P10415

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 4 von Hippel-Lindau disease tumor suppressor × 1 （P40337） Elongin-B × 1 （Q15370） Elongin-C × 1 （Q15369） ;N-({4-[2-(4-{[(4R)-4'-chloro-4-methyl-6-{[4-(4-{[4-{[(2R)-4-[(1R,4R)-2-oxa-5-azabicyclo[2.2.1]heptan-5-yl]-1-(phenylsulfanyl)butan-2-yl]amino}-3-(trifluoromethanesulfonyl)benzene-1-sulfonyl]carbamoyl}phenyl)piperazin-1-yl]methyl}-2,3,4,5-tetrahydro[1,1'-biphenyl]-4-yl]methyl}piperazin-1-yl)-2-oxoethyl]piperazin-1-yl}acetyl)-3-methyl-L-valyl-(4S)-4-hydroxy-N-{(1S)-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl}-L-prolinamide ; × 1 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
1ysw 2o2f 2w3l 2w3l 4lvt 4lvt 4lxd 4man 4man 6gl8 7lhb 7lhb

13 assemblies; showing the first 12

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1g5m 1gjh 2o21 2o22 2xa0 2xa0 4aq3 4aq3 4aq3 4aq3 4aq3 4aq3

67 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name BCL2_HUMAN
Isoform —
PDB entities 4
Chains and sequence ranges Author chain D； PDBConstruct 3–209； UniProt 1–207

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_id8fy2
Deposition date deposition_date2023-01-25
Last revision last_revision2024-04-10
Structure title titleE3:PROTAC:target ternary complex structure (VCB/WH244/BCL-2)
Keywords keywordsternary complex, degrader, TRANSCRIPTION; TRANSCRIPTION
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.

8fy2__assembly_1__model_1

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

Download this curve (.dat)

8fy2__assembly_1__model_1 | I(q)

10-2 10-1 105 106 107 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

8fy2__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）34.49 Å
Rg (electron density)34.64 Å
Total Rg34.77 Å
Atom count4022
Residues480
Excluded volume71684 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 8fy2__assembly_1__model_1 tetrameric （4） 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 (5)

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7. Citations (1)