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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.68 Å
R-Value Free:
0.259 (Depositor), 0.270 (DCC)
R-Value Work:
0.213 (Depositor), 0.230 (DCC)
R-Value Observed:
0.216 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

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.

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

Find similar proteins by:

(by identity cutoff) | 3D Structure

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 GTEx: ENSG00000167005
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O43809
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
RWG (Subject of Investigation/LOI) Query on RWG Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A]	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		Interactions Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B]	C [auth A] D [auth A] I [auth B] J [auth B] K [auth B] C [auth A], D [auth A], I [auth B], J [auth B], K [auth B], L [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain M [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain M [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain M [auth B]	E [auth A], F [auth A], M [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain M [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain M [auth B]