5R4S | pdb_00005r4s

PanDDA analysis group deposition -- Crystal Structure of HUMAN CLEAVAGE FACTOR IM in complex with EN08775-45

PDB DOI: https://doi.org/10.2210/pdb5R4S/pdb
Deposition Group: G_1002126 (changed state) | Explore G_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: 1.61 Å
R-Value Free:
0.248 (Depositor), 0.251 (DCC)
R-Value Work:
0.209 (Depositor), 0.222 (DCC)
R-Value Observed:
0.211 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 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: 46.59 kDa
Atom Count: 3,522
Modeled Residue Count: 394
Deposited Residue Count: 394
Unique protein chains: 1

Macromolecules

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| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O43809
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
RWD (Subject of Investigation/LOI) Query on RWD Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	(4S,5R)-4-hydroxy-5-methyl-5-[(1-phenyl-1H-1,2,3-triazol-4-yl)methyl]pyrrolidin-2-one C₁₄ H₁₆ N₄ O₂ UILOQPSPJQYNHO-GXTWGEPZSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain H [auth B] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain I [auth B] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain H [auth B] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain I [auth B] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain H [auth B] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A] E [auth A] H [auth B] I [auth B] J [auth B] D [auth A], E [auth A], H [auth B], I [auth B], J [auth B], K [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain L [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain L [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A], G [auth A], L [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain L [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain L [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.61 Å
R-Value Free: 0.248 (Depositor), 0.251 (DCC)
R-Value Work: 0.209 (Depositor), 0.222 (DCC)
R-Value Observed: 0.211 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.91	α = 90
b = 58.91	β = 90
c = 212.33	γ = 120

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2020-07-08

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2020-07-08
Type: Initial release
Version 1.1: 2024-03-06
Changes: Data collection, Database references, Derived calculations
Version 1.2: 2026-02-18
Changes: Refinement description, Structure summary

5R4S | pdb_00005r4s

PanDDA analysis group deposition -- Crystal Structure of HUMAN CLEAVAGE FACTOR IM in complex with EN08775-45

Literature

PanDDA analysis group deposition

Biological Assembly 1

Biological Assembly 2

Macromolecules

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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