6QP5 | pdb_00006qp5

Apo Human Calcium/Calmodulin-dependent kinase type 1D

• PDB DOI: https://doi.org/10.2210/pdb6QP5/pdb

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


• Deposited: 2019-02-13 Released: 2020-03-04 
• Deposition Author(s): Sorrell, F.J., Knapp, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.227 (Depositor), 0.229 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.196 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Starting Model: experimental

Literature

Apo Human Calcium/Calmodulin-dependent kinase type 1D

Sorrell, F.J., Knapp, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: gel filtration, equilibrium centrifugation

Macromolecule Content 

• Total Structure Weight: 37.02 kDa 
• Atom Count: 2,311 
• Modeled Residue Count: 266 
• Deposited Residue Count: 322 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Calcium/calmodulin-dependent protein kinase type 1D	A	322	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
SO4	B [auth A], C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	D [auth A], E [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.227 (Depositor), 0.229 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.196 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.11	α = 90
b = 45.79	β = 105.8
c = 107.931	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
xia2	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-03-04 
Deposition Author(s): Sorrell, F.J., Knapp, S.

Revision History  

• Version 1.0: 2020-03-04
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description