Download MendeleyCrystal structure of pVHL:ElonginC:ElonginB complex bound to PROTAC JW48
Kraemer, A., Weckesser, J., Knapp, S., Structural Genomics Consortium (SGC)To be published.
8C13
Crystal structure of pVHL:ElonginC:ElonginB complex bound to PROTAC JW48
- PDB DOI: https://doi.org/10.2210/pdb8C13/pdb
- Classification: LIGASE
- Organism(s): Homo sapiens
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2022-12-20 Released: 2022-12-28
- Funding Organization(s): The Structural Genomics Consortium (SGC)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.30 Å
- R-Value Free: 0.261
- R-Value Work: 0.223
This is version 1.0 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Elongin-B | A [auth J] | 118 | Homo sapiens | Mutation(s): 0 Gene Names: ELOB, TCEB2 |  |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for Q15370 (Homo sapiens) Explore Q15370 Go to UniProtKB: Q15370 | |||||
PHAROS: Q15370 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q15370 | ||||
Protein Feature ViewExpand | |||||
| |||||
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Elongin-C | B [auth K] | 112 | Homo sapiens | Mutation(s): 0 Gene Names: ELOC, TCEB1 |  |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for Q15369 (Homo sapiens) Explore Q15369 Go to UniProtKB: Q15369 | |||||
PHAROS: Q15369 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q15369 | ||||
Protein Feature ViewExpand | |||||
| |||||
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| von Hippel-Lindau disease tumor suppressor | C [auth L] | 160 | Homo sapiens | Mutation(s): 0 Gene Names: VHL |  |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P40337 (Homo sapiens) Explore P40337 Go to UniProtKB: P40337 | |||||
PHAROS: P40337 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P40337 | ||||
Protein Feature ViewExpand | |||||
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Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| SYF (Subject of Investigation/LOI) Query on SYF | D [auth L] | (2~{S},4~{R})-1-[(2~{S})-2-[3-[2-[2-[2-(acetamidomethyl)-4-(6,7-dihydro-5~{H}-pyrrolo[1,2-a]imidazol-2-yl)phenoxy]ethoxy]ethoxy]propanoylamino]-3,3-dimethyl-butanoyl]-~{N}-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide C44 H57 N7 O8 S DZVPJUGTNDKRRC-ZAZQKZRESA-N |  | Ligand Interaction | |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.30 Å
- R-Value Free: 0.261
- R-Value Work: 0.223
- Space Group: C 1 2 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 73.797 | α = 90 |
| b = 60.787 | β = 100.58 |
| c = 97.228 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| Aimless | data scaling |
| MOLREP | phasing |
| XDS | data reduction |
Entry History & Funding Information
Deposition Data
- Released Date: 2022-12-28 Deposition Author(s): Kraemer, A., Weckesser, J., Knapp, S., Structural Genomics Consortium (SGC)
| Funding Organization | Location | Grant Number |
|---|---|---|
| The Structural Genomics Consortium (SGC) | Canada | -- |
Revision History (Full details and data files)
- Version 1.0: 2022-12-28
Type: Initial release
