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6hax

Crystal structure of PROTAC 2 in complex with the bromodomain of human SMARCA2 and pVHL:ElonginC:ElonginB

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

Probable global transcription activator SNF2L2

Homo sapiens

UniProt P51531

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） Elongin-B × 1 （Q15370） 1,2-ETHANEDIOL × 8 ;(2~{S},4~{R})-~{N}-[[2-[2-[4-[[4-[3-azanyl-6-(2-hydroxyphenyl)pyridazin-4-yl]piperazin-1-yl]methyl]phenyl]ethoxy]-4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-1-[(2~{S})-2-[(1-fluoranylcyclopropyl)carbonylamino]-3,3-dimethyl-butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide ; × 1 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 water × 4 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 4 von Hippel-Lindau disease tumor suppressor × 1 （P40337） Elongin-C × 1 （Q15369） Elongin-B × 1 （Q15370） 1,2-ETHANEDIOL × 6 ;(2~{S},4~{R})-~{N}-[[2-[2-[4-[[4-[3-azanyl-6-(2-hydroxyphenyl)pyridazin-4-yl]piperazin-1-yl]methyl]phenyl]ethoxy]-4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-1-[(2~{S})-2-[(1-fluoranylcyclopropyl)carbonylamino]-3,3-dimethyl-butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide ; × 1 water × 4 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
2dat 5dkc 5dkh 5dkh 5dkh 7z78 7z78 7z78 8qjt 8qjt 8qjt 9ayq

34 assemblies; showing the first 12

Homodimer
6haz

1 assemblies

Homotetramer

None

Other homooligomers
9du0

1 assemblies

Heteromeric or nucleic-acid complex
6eg2 6eg3 6hax 6hax 6hay 6hay 7z6l 7z76 7z77 9dty 9hyb 9hyb

27 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name SMCA2_HUMAN
Isoform P51531-2
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 3–123； UniProt 1373–1493 Author chain E； PDBConstruct 3–123； UniProt 1373–1493

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 Probable global transcription activator SNF2L2 × 1 （P51531） Elongin-C × 1 （Q15369） Elongin-B × 1 （Q15370） 1,2-ETHANEDIOL × 8 ;(2~{S},4~{R})-~{N}-[[2-[2-[4-[[4-[3-azanyl-6-(2-hydroxyphenyl)pyridazin-4-yl]piperazin-1-yl]methyl]phenyl]ethoxy]-4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-1-[(2~{S})-2-[(1-fluoranylcyclopropyl)carbonylamino]-3,3-dimethyl-butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide ; × 1 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 water × 4 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 4 Probable global transcription activator SNF2L2 × 1 （P51531） Elongin-C × 1 （Q15369） Elongin-B × 1 （Q15370） 1,2-ETHANEDIOL × 6 ;(2~{S},4~{R})-~{N}-[[2-[2-[4-[[4-[3-azanyl-6-(2-hydroxyphenyl)pyridazin-4-yl]piperazin-1-yl]methyl]phenyl]ethoxy]-4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-1-[(2~{S})-2-[(1-fluoranylcyclopropyl)carbonylamino]-3,3-dimethyl-butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide ; × 1 water × 4 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 2
Chains and sequence ranges Author chain B； PDBConstruct 3–162； UniProt 54–213 Author chain F； PDBConstruct 3–162； UniProt 54–213

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 Probable global transcription activator SNF2L2 × 1 （P51531） von Hippel-Lindau disease tumor suppressor × 1 （P40337） Elongin-B × 1 （Q15370） 1,2-ETHANEDIOL × 8 ;(2~{S},4~{R})-~{N}-[[2-[2-[4-[[4-[3-azanyl-6-(2-hydroxyphenyl)pyridazin-4-yl]piperazin-1-yl]methyl]phenyl]ethoxy]-4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-1-[(2~{S})-2-[(1-fluoranylcyclopropyl)carbonylamino]-3,3-dimethyl-butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide ; × 1 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 water × 4 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 4 Probable global transcription activator SNF2L2 × 1 （P51531） von Hippel-Lindau disease tumor suppressor × 1 （P40337） Elongin-B × 1 （Q15370） 1,2-ETHANEDIOL × 6 ;(2~{S},4~{R})-~{N}-[[2-[2-[4-[[4-[3-azanyl-6-(2-hydroxyphenyl)pyridazin-4-yl]piperazin-1-yl]methyl]phenyl]ethoxy]-4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-1-[(2~{S})-2-[(1-fluoranylcyclopropyl)carbonylamino]-3,3-dimethyl-butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide ; × 1 water × 4 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 2–97； UniProt 17–112 Author chain G； PDBConstruct 2–97； UniProt 17–112

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 Probable global transcription activator SNF2L2 × 1 （P51531） von Hippel-Lindau disease tumor suppressor × 1 （P40337） Elongin-C × 1 （Q15369） 1,2-ETHANEDIOL × 8 ;(2~{S},4~{R})-~{N}-[[2-[2-[4-[[4-[3-azanyl-6-(2-hydroxyphenyl)pyridazin-4-yl]piperazin-1-yl]methyl]phenyl]ethoxy]-4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-1-[(2~{S})-2-[(1-fluoranylcyclopropyl)carbonylamino]-3,3-dimethyl-butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide ; × 1 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 water × 4 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 4 Probable global transcription activator SNF2L2 × 1 （P51531） von Hippel-Lindau disease tumor suppressor × 1 （P40337） Elongin-C × 1 （Q15369） 1,2-ETHANEDIOL × 6 ;(2~{S},4~{R})-~{N}-[[2-[2-[4-[[4-[3-azanyl-6-(2-hydroxyphenyl)pyridazin-4-yl]piperazin-1-yl]methyl]phenyl]ethoxy]-4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-1-[(2~{S})-2-[(1-fluoranylcyclopropyl)carbonylamino]-3,3-dimethyl-butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide ; × 1 water × 4 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 Q15370-2
PDB entities 4
Chains and sequence ranges Author chain D； PDBConstruct 1–104； UniProt 1–104 Author chain H； PDBConstruct 1–104； UniProt 1–104

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_id6hax
Deposition date deposition_date2018-08-09
Structure title titleCrystal structure of PROTAC 2 in complex with the bromodomain of human SMARCA2 and pVHL:ElonginC:ElonginB
Keywords keywordsbromodomain, E3 Ubiquitin Protein Ligase, GENE REGULATION; GENE REGULATION
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.

6hax__assembly_1__model_1

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

Download this curve (.dat)

6hax__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.

6hax__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）31.83 Å
Rg (electron density)31.88 Å
Total Rg32.24 Å
Atom count3745
Residues456
Excluded volume66962 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 6hax__assembly_1__model_1 tetrameric （4） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 6hax__assembly_2__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 (8)

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6. Fold Classification (SCOP + CATH) 21 domains

SCOP 2.08 (11 domains)

Domain ID domain_idd6haxa_
Class classa — All alpha proteins
Fold Fold folda.29 — Bromodomain-like
Superfamily Superfamily superfamilya.29.2 — Bromodomain
Family Family familya.29.2.0 — automated matches
Domain ID domain_idd6haxb_
Class classb — All beta proteins
Fold Fold foldb.3 — Prealbumin-like
Superfamily Superfamily superfamilyb.3.3 — VHL
Family Family familyb.3.3.1 — VHL
Domain ID domain_idd6haxc1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.42 — POZ domain
Superfamily Superfamily superfamilyd.42.1 — POZ domain
Family Family familyd.42.1.1 — BTB/POZ domain
Domain ID domain_idd6haxc2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd6haxd_
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.15.1.1 — Ubiquitin-related
Domain ID domain_idd6haxe1
Class classa — All alpha proteins
Fold Fold folda.29 — Bromodomain-like
Superfamily Superfamily superfamilya.29.2 — Bromodomain
Family Family familya.29.2.0 — automated matches
Domain ID domain_idd6haxe2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd6haxf_
Class classb — All beta proteins
Fold Fold foldb.3 — Prealbumin-like
Superfamily Superfamily superfamilyb.3.3 — VHL
Family Family familyb.3.3.1 — VHL
Domain ID domain_idd6haxg1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.42 — POZ domain
Superfamily Superfamily superfamilyd.42.1 — POZ domain
Family Family familyd.42.1.1 — BTB/POZ domain
Domain ID domain_idd6haxg2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd6haxh_
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.15.1.1 — Ubiquitin-related

CATH v4.4 (10 domains)

Domain ID domain_id6haxA00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology920 — Histone Acetyltransferase; Chain A
Homologous superfamily homologous superfamily10 — Bromodomain-like
Domain ID domain_id6haxB01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily780 — von Hippel-Lindau disease tumour suppressor, beta domain
Domain ID domain_id6haxB02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology750 — Elongin C; Chain C, domain 1
Homologous superfamily homologous superfamily10 — von Hippel-Lindau disease tumour suppressor, alpha domain
Domain ID domain_id6haxC00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology710 — Potassium Channel Kv1.1; Chain A
Homologous superfamily homologous superfamily10 — Potassium Channel Kv1.1; Chain A
Domain ID domain_id6haxD00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
Domain ID domain_id6haxE00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology920 — Histone Acetyltransferase; Chain A
Homologous superfamily homologous superfamily10 — Bromodomain-like
Domain ID domain_id6haxF01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily780 — von Hippel-Lindau disease tumour suppressor, beta domain
Domain ID domain_id6haxF02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology750 — Elongin C; Chain C, domain 1
Homologous superfamily homologous superfamily10 — von Hippel-Lindau disease tumour suppressor, alpha domain
Domain ID domain_id6haxG00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology710 — Potassium Channel Kv1.1; Chain A
Homologous superfamily homologous superfamily10 — Potassium Channel Kv1.1; Chain A
Domain ID domain_id6haxH00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
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7. Citations (1)