9IPW | pdb_00009ipw

Crystal structure of VHL-EloB-EloC in complex with a fragment compound 7HC_5(D3)

• PDB DOI: https://doi.org/10.2210/pdb9IPW/pdb

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-07-11 Released: 2025-01-29 
• Deposition Author(s): Lee, B.I., Kim, Y.
• Funding Organization(s): National Research Foundation (NRF, Korea), Other government

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.273 (Depositor), 0.272 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.208 (DCC) 
• R-Value Observed: 
  0.210 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of VHL-EloB-EloC in complex with a fragment compound 7HC_5(D3)

Lee, B.I., Kim, Y.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 4 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 167.16 kDa 
• Atom Count: 10,223 
• Modelled Residue Count: 1,263 
• Deposited Residue Count: 1,452 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Elongin-B	A, D, G, J	104	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 GTEx:  ENSG00000103363

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Elongin-C	B, E, H, K	97	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 GTEx:  ENSG00000154582

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
von Hippel-Lindau disease tumor suppressor	C, F, I, L	162	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 GTEx:  ENSG00000134086

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1L2Z (Subject of Investigation/LOI)	M [auth K]	7-Hydroxy-4-methoxymethylcoumarin C11 H10 O4 PRVOZGKAZHXKMM-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CAS	A, D, G, J	L-PEPTIDE LINKING	C5 H12 As N O2 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.273 (Depositor), 0.272 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.208 (DCC) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: P 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.443	α = 90
b = 94.443	β = 90
c = 361.486	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-01-29 
Deposition Author(s): Lee, B.I., Kim, Y.

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Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	--
Other government		--

Revision History  

• Version 1.0: 2025-01-29
  Type: Initial release