9Q3O | pdb_00009q3o

Crystal structure of human CDK5-cyclinB1 complex bound to AMP-PNP

• PDB DOI: https://doi.org/10.2210/pdb9Q3O/pdb

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


• Deposited: 2025-08-19 Released: 2026-08-26 
• Deposition Author(s): Syed, A., Arvai, A.S., Chowdhury, D., Tainer, J.A.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.249 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.197 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of human CDK5-cyclinB1 complex bound to AMP-PNP

Syed, A., Arvai, A.S., Chowdhury, D., Tainer, J.A.

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 Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 69.59 kDa 
• Atom Count: 4,710 
• Modeled Residue Count: 559 
• Deposited Residue Count: 580 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclin-dependent kinase 5	A [auth B]	295	Homo sapiens	Mutation(s): 0  Gene Names: CDK5, CDKN5, PSSALRE EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q00535 (Homo sapiens) Explore Q00535  Go to UniProtKB:  Q00535
PHAROS:  Q00535 GTEx:  ENSG00000164885

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
G2/mitotic-specific cyclin-B1	B [auth C]	285	Homo sapiens	Mutation(s): 3  Gene Names: CCNB1, CCNB
UniProt & NIH Common Fund Data Resources
Find proteins for P14635 (Homo sapiens) Explore P14635  Go to UniProtKB:  P14635
PHAROS:  P14635 GTEx:  ENSG00000134057

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
P4K	D [auth B], G [auth C], H [auth C], I [auth C]	polyethylene glycol C30 H62 O15 WWPGFZAAWXFBTF-UHFFFAOYSA-N
ANP (Subject of Investigation/LOI)	E [auth B]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C10 H17 N6 O12 P3 PVKSNHVPLWYQGJ-KQYNXXCUSA-N
SO4	C [auth B], F [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	J [auth C], K [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.249 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.197 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.859	α = 90
b = 120.859	β = 90
c = 116.07	γ = 120

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: 2026-08-26 
Deposition Author(s): Syed, A., Arvai, A.S., Chowdhury, D., Tainer, J.A.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	P01 CA092584
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	R35 CA220430

Revision History  

• Version 1.0: 2026-08-26
  Type: Initial release