← Back to search
9snp

VHL/Elongin B/Elongin C complex with compound 60

Method: X-RAY DIFFRACTION
▼

1. Protein Identity and Related Structures Protein Identity & Related Structures

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 3 Elongin-C × 1 （Q15369） von Hippel-Lindau disease tumor suppressor × 1 （P40337） ;(2~{S},4~{R})-1-[(2~{R})-2-[3-[2-(2-methoxyethoxy)ethoxy]-1,2-oxazol-5-yl]-3-methyl-butanoyl]-~{N}-[(1~{S})-1-[4-(2-methylimidazol-1-yl)phenyl]ethyl]-4-oxidanyl-pyrrolidine-2-carboxamide ; × 1 water × 3 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 3 Elongin-C × 1 （Q15369） von Hippel-Lindau disease tumor suppressor × 1 （P40337） ;(2~{S},4~{R})-1-[(2~{R})-2-[3-[2-(2-methoxyethoxy)ethoxy]-1,2-oxazol-5-yl]-3-methyl-butanoyl]-~{N}-[(1~{S})-1-[4-(2-methylimidazol-1-yl)phenyl]ethyl]-4-oxidanyl-pyrrolidine-2-carboxamide ; × 1 water × 3 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 3 Elongin-C × 1 （Q15369） von Hippel-Lindau disease tumor suppressor × 1 （P40337） ;(2~{S},4~{R})-1-[(2~{R})-2-[3-[2-(2-methoxyethoxy)ethoxy]-1,2-oxazol-5-yl]-3-methyl-butanoyl]-~{N}-[(1~{S})-1-[4-(2-methylimidazol-1-yl)phenyl]ethyl]-4-oxidanyl-pyrrolidine-2-carboxamide ; × 1 water × 3 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 3 Elongin-C × 1 （Q15369） von Hippel-Lindau disease tumor suppressor × 1 （P40337） ;(2~{S},4~{R})-1-[(2~{R})-2-[3-[2-(2-methoxyethoxy)ethoxy]-1,2-oxazol-5-yl]-3-methyl-butanoyl]-~{N}-[(1~{S})-1-[4-(2-methylimidazol-1-yl)phenyl]ethyl]-4-oxidanyl-pyrrolidine-2-carboxamide ; × 1 water × 3 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 1
Chains and sequence ranges Author chain A； PDBConstruct 1–104； UniProt 1–104 Author chain D； PDBConstruct 1–104； UniProt 1–104 Author chain G； PDBConstruct 1–104； UniProt 1–104 Author chain J； PDBConstruct 1–104； UniProt 1–104

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 3 Elongin-B × 1 （Q15370） von Hippel-Lindau disease tumor suppressor × 1 （P40337） ;(2~{S},4~{R})-1-[(2~{R})-2-[3-[2-(2-methoxyethoxy)ethoxy]-1,2-oxazol-5-yl]-3-methyl-butanoyl]-~{N}-[(1~{S})-1-[4-(2-methylimidazol-1-yl)phenyl]ethyl]-4-oxidanyl-pyrrolidine-2-carboxamide ; × 1 water × 3 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 3 Elongin-B × 1 （Q15370） von Hippel-Lindau disease tumor suppressor × 1 （P40337） ;(2~{S},4~{R})-1-[(2~{R})-2-[3-[2-(2-methoxyethoxy)ethoxy]-1,2-oxazol-5-yl]-3-methyl-butanoyl]-~{N}-[(1~{S})-1-[4-(2-methylimidazol-1-yl)phenyl]ethyl]-4-oxidanyl-pyrrolidine-2-carboxamide ; × 1 water × 3 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 3 Elongin-B × 1 （Q15370） von Hippel-Lindau disease tumor suppressor × 1 （P40337） ;(2~{S},4~{R})-1-[(2~{R})-2-[3-[2-(2-methoxyethoxy)ethoxy]-1,2-oxazol-5-yl]-3-methyl-butanoyl]-~{N}-[(1~{S})-1-[4-(2-methylimidazol-1-yl)phenyl]ethyl]-4-oxidanyl-pyrrolidine-2-carboxamide ; × 1 water × 3 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 3 Elongin-B × 1 （Q15370） von Hippel-Lindau disease tumor suppressor × 1 （P40337） ;(2~{S},4~{R})-1-[(2~{R})-2-[3-[2-(2-methoxyethoxy)ethoxy]-1,2-oxazol-5-yl]-3-methyl-butanoyl]-~{N}-[(1~{S})-1-[4-(2-methylimidazol-1-yl)phenyl]ethyl]-4-oxidanyl-pyrrolidine-2-carboxamide ; × 1 water × 3 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 2
Chains and sequence ranges Author chain B； PDBConstruct 2–97； UniProt 17–112 Author chain E； PDBConstruct 2–97； UniProt 17–112 Author chain H； PDBConstruct 2–97； UniProt 17–112 Author chain K； PDBConstruct 2–97； UniProt 17–112

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 3 Elongin-B × 1 （Q15370） Elongin-C × 1 （Q15369） ;(2~{S},4~{R})-1-[(2~{R})-2-[3-[2-(2-methoxyethoxy)ethoxy]-1,2-oxazol-5-yl]-3-methyl-butanoyl]-~{N}-[(1~{S})-1-[4-(2-methylimidazol-1-yl)phenyl]ethyl]-4-oxidanyl-pyrrolidine-2-carboxamide ; × 1 water × 3 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 3 Elongin-B × 1 （Q15370） Elongin-C × 1 （Q15369） ;(2~{S},4~{R})-1-[(2~{R})-2-[3-[2-(2-methoxyethoxy)ethoxy]-1,2-oxazol-5-yl]-3-methyl-butanoyl]-~{N}-[(1~{S})-1-[4-(2-methylimidazol-1-yl)phenyl]ethyl]-4-oxidanyl-pyrrolidine-2-carboxamide ; × 1 water × 3 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 3 Elongin-B × 1 （Q15370） Elongin-C × 1 （Q15369） ;(2~{S},4~{R})-1-[(2~{R})-2-[3-[2-(2-methoxyethoxy)ethoxy]-1,2-oxazol-5-yl]-3-methyl-butanoyl]-~{N}-[(1~{S})-1-[4-(2-methylimidazol-1-yl)phenyl]ethyl]-4-oxidanyl-pyrrolidine-2-carboxamide ; × 1 water × 3 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 3 Elongin-B × 1 （Q15370） Elongin-C × 1 （Q15369） ;(2~{S},4~{R})-1-[(2~{R})-2-[3-[2-(2-methoxyethoxy)ethoxy]-1,2-oxazol-5-yl]-3-methyl-butanoyl]-~{N}-[(1~{S})-1-[4-(2-methylimidazol-1-yl)phenyl]ethyl]-4-oxidanyl-pyrrolidine-2-carboxamide ; × 1 water × 3 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 3
Chains and sequence ranges Author chain C； PDBConstruct 3–162； UniProt 54–213 Author chain F； PDBConstruct 3–162； UniProt 54–213 Author chain I； PDBConstruct 3–162； UniProt 54–213 Author chain L； PDBConstruct 3–162； UniProt 54–213

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id9snp
Deposition date deposition_date2025-09-11
Last revision last_revision2026-04-01
Structure title titleVHL/Elongin B/Elongin C complex with compound 60
Keywords keywordsE3 Ligase, Complex, PROTAC, LIGASE; LIGASE
Experimental Method methodX-RAY DIFFRACTION
▼

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.

9snp__assembly_1__model_1

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

Download this curve (.dat)

9snp__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.

9snp__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）24.67 Å
Rg (electron density)23.69 Å
Total Rg24.29 Å
Atom count2696
Residues330
Excluded volume48063 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 9snp__assembly_1__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 9snp__assembly_2__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 9snp__assembly_3__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
4 1 9snp__assembly_4__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (5)

▶

7. Citations (1)