8BFM | pdb_00008bfm

Crystal structure of human calmodulin-dependent protein kinase 1D (CAMK1D) in complex with FZ331

• PDB DOI: https://doi.org/10.2210/pdb8BFM/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-10-26 Released: 2022-11-23 
• Deposition Author(s): Kraemer, A., Zhu, W.F., Hernandez-Olmos, V., Proschak, E., Knapp, S., Structural Genomics Consortium (SGC)
• Funding Organization(s): The Structural Genomics Consortium (SGC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.224 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.201 (Depositor) 

Starting Model: experimental

Literature

Structure of human WDR5 and pVHL:ElonginC:ElonginB bound to PROTAC with PEG linker (conformation #2)

Kraemer, A., Doelle, A., Knapp, S., Structural Genomics Consortium (SGC)

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 43.82 kDa 
• Atom Count: 2,214 
• Modeled Residue Count: 265 
• Deposited Residue Count: 385 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Calcium/calmodulin-dependent protein kinase type 1D	A	385	Homo sapiens	Mutation(s): 0  Gene Names: CAMK1D, CAMKID EC: 2.7.11.17
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IU85 (Homo sapiens) Explore Q8IU85  Go to UniProtKB:  Q8IU85
PHAROS:  Q8IU85 GTEx:  ENSG00000183049

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
QI6 (Subject of Investigation/LOI)	D [auth A], E [auth A]	pyrazolo[5,1-a]phthalazin-6-amine C10 H8 N4 VOLKDTKFDOIYJN-UHFFFAOYSA-N
SO4	B [auth A], C [auth A], F [auth A], G [auth A], H [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.224 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.201 (Depositor) 

Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.531	α = 90
b = 44.8	β = 104.26
c = 108.589	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-11-23 
Deposition Author(s): Kraemer, A., Zhu, W.F., Hernandez-Olmos, V., Proschak, E., Knapp, S., Structural Genomics Consortium (SGC)

---

Funding Organization	Location	Grant Number
The Structural Genomics Consortium (SGC)	Canada	--

Revision History  

• Version 1.0: 2022-11-23
  Type: Initial release
  
• Version 2.0: 2023-05-24
  Changes: Non-polymer description
• Version 2.1: 2024-02-07
  Changes: Data collection, Refinement description