Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Dihedral - D6  (3D View)
Global Stoichiometry: Homo 12-mer - A12 

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

Biological Assembly Evidence: authors reported there is no experimental evidence

Macromolecule Content

• Total Structure Weight: 811029.13 
• Atom Count: 48408 
• Residue Count: 7272 
• Unique protein chains: 1

6MCK

p97 D1D2 with CB5083 bound

• DOI: 10.2210/pdb6MCK/pdb

• Classification: CHAPERONE Hydrolase
• Organism(s): Homo sapiens
• Expression System: Escherichia coli


• Deposited: 2018-08-31 Released: 2019-01-23 
• Deposition Author(s): Xia, D., Tang, W.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.77 Å
• R-Value Free: 0.265 
• R-Value Work: 0.222 

Literature

Structural Basis of p97 Inhibition by the Site-Selective Anticancer Compound CB-5083.

Tang, W.K., Odzorig, T., Jin, W., Xia, D.

(2019) Mol. Pharmacol. 95: 286-293

• PubMed: 30591537 

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Transitional endoplasmic reticulum ATPase	A, B, C, D, E, F, G, H, I, J, K, L	606	Homo sapiens	Mutation(s): 0  Gene Names: VCP EC: 3.6.4.6
Find proteins for P55072 (Homo sapiens) Go to Gene View: VCP Go to UniProtKB:  P55072

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
JDP	A, B, C, D, E, F, G, H, I, J, K, L	1-[4-(benzylamino)-7,8-dihydro-5H-pyrano[4,3-d]pyrimidin-2-yl]-2-methyl-1H-indole-4-carboxamide C24 H23 N5 O2 RDALZZCKQFLGJP-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.77 Å
• R-Value Free: 0.265 
• R-Value Work: 0.222 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 127.410	α = 90.00
b = 263.830	β = 103.67
c = 164.130	γ = 90.00

Software Package:

Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2018-08-31 
• Released Date: 2019-01-23 
• Deposition Author(s): Xia, D., Tang, W.K.

Revision History 

• Version 1.0: 2019-01-23
  Type: Initial release
• Version 1.1: 2019-01-30
  Type: Data collection, Database references
• Version 1.2: 2019-02-13
  Type: Data collection, Database references