1PKD | pdb_00001pkd

THE CRYSTAL STRUCTURE OF UCN-01 IN COMPLEX WITH PHOSPHO-CDK2/CYCLIN A

• PDB DOI: https://doi.org/10.2210/pdb1PKD/pdb

• Classification: TRANSFERASE/CELL CYCLE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2003-06-05 Released: 2003-06-24 
• Deposition Author(s): Johnson, L.N., De Moliner, E., Brown, N.R., Song, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.268 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.215 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.218 (Depositor) 

Starting Model: experimental

Literature

The Crystal Structure of UCN-01 in Complex with Phospho-CDK2/Cyclin A

Johnson, L.N., De Moliner, E., Brown, N.R., Song, H.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content 

• Total Structure Weight: 127.96 kDa 
• Atom Count: 9,416 
• Modeled Residue Count: 1,110 
• Deposited Residue Count: 1,110 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cell division protein kinase 2	A, C	297	Homo sapiens	Mutation(s): 1  Gene Names: CDK2 EC: 2.7.1 (PDB Primary Data), 2.7.11.22 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P24941 (Homo sapiens) Explore P24941  Go to UniProtKB:  P24941
PHAROS:  P24941 GTEx:  ENSG00000123374

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclin A2	B, D	258	Homo sapiens	Mutation(s): 0  Gene Names: CCNA2 OR CCNA OR CCN1
UniProt & NIH Common Fund Data Resources
Find proteins for P20248 (Homo sapiens) Explore P20248  Go to UniProtKB:  P20248
PHAROS:  P20248 GTEx:  ENSG00000145386

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UCN	E [auth A], F [auth C]	7-HYDROXYSTAUROSPORINE C28 H26 N4 O4 PBCZSGKMGDDXIJ-HQCWYSJUSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TPO	A, C	L-PEPTIDE LINKING	C4 H10 N O6 P		THR

Binding Affinity Annotations
ID	Source	Binding Affinity
UCN	BindingDB:  1PKD	Ki: min: 30, max: 95 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.268 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.215 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.218 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.62	α = 90
b = 134.57	β = 90
c = 147.97	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-06-24 
Deposition Author(s): Johnson, L.N., De Moliner, E., Brown, N.R., Song, H.

Revision History  

• Version 1.0: 2003-06-24
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-01-31
  Changes: Database references
• Version 1.4: 2023-08-16
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.5: 2024-11-13
  Changes: Structure summary