5R4T

PanDDA analysis group deposition -- Crystal Structure of HUMAN CLEAVAGE FACTOR IM in complex with SK-430

• PDB DOI:  https://doi.org/10.2210/pdb5R4T/pdb
• Deposition Group: G_1002126 (changed state) ExploreG_1002126

• Classification: RNA BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-02-27 Released: 2020-07-08 
• Deposition Author(s): Kidd, S.L., Mateu, N., Talon, R., Krojer, T., Aimon, A., Bradley, A.R., Fairhead, M., Diaz-Saez, L., Sore, H.F., Madin, A., Huber, K.V.M., von Delft, F., Spring, D.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.68 Å
• R-Value Free: 0.259 
• R-Value Work: 0.213 
• R-Value Observed: 0.216 

Literature

PanDDA analysis group deposition

Kidd, S.L., Mateu, N., Talon, R., Krojer, T., Aimon, A., Bradley, A.R., Fairhead, M., Diaz-Saez, L., Sore, H.F., Madin, A., Huber, K.V.M., von Delft, F., Spring, D.R.

To be published.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

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

Macromolecule Content

• Total Structure Weight: 46.89 kDa 
• Atom Count: 3,545 
• Modelled Residue Count: 394 
• Deposited Residue Count: 394 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cleavage and polyadenylation specificity factor subunit 5	A, B	197	Homo sapiens	Mutation(s): 0  Gene Names: NUDT21, CFIM25, CPSF25, CPSF5
UniProt & NIH Common Fund Data Resources
Find proteins for O43809 (Homo sapiens) Explore O43809  Go to UniProtKB:  O43809
PHAROS:  O43809

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RWG (Subject of Investigation/LOI)	G [auth A], H [auth A]	(5R)-5-{[1-(4-fluorophenyl)-1H-1,2,3-triazol-4-yl]methyl}-5-methylpyrrolidine-2,4-dione C14 H13 F N4 O2 UUBOMXRWPFJYHC-CQSZACIVSA-N
ZN	C [auth A], D [auth A], I [auth B], J [auth B], K [auth B], L [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT	E [auth A], F [auth A], M [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.68 Å
• R-Value Free: 0.259 
• R-Value Work: 0.213 
• R-Value Observed: 0.216 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.01	α = 90
b = 59.01	β = 90
c = 212.964	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-07-08 
Deposition Author(s): Kidd, S.L., Mateu, N., Talon, R., Krojer, T., Aimon, A., Bradley, A.R., Fairhead, M., Diaz-Saez, L., Sore, H.F., Madin, A., Huber, K.V.M., von Delft, F., Spring, D.R.

Revision History  

• Version 1.0: 2020-07-08
  Type: Initial release