9D4E | pdb_00009d4e

Crystal structure of the human DCAF1 WDR domain in complex with OICR-41103

PDB DOI: https://doi.org/10.2210/pdb9D4E/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): Yes

Deposited: 2024-08-12 Released: 2024-12-18
Deposition Author(s): Kimani, S., Dong, A., Li, Y., Seitova, A., Al-awar, R., Mamai, A., Ackloo, S., Arrowsmith, C.H., Edwards, A.M., Halabelian, L., Structural Genomics Consortium (SGC)
Funding Organization(s): Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.206 (Depositor), 0.214 (DCC)
R-Value Work:
0.178 (Depositor), 0.187 (DCC)
R-Value Observed:
0.180 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

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Literature

Crystal structure of the human DCAF1 WDR domain in complex with OICR-1103

Kimani, S., Dong, A., Li, Y., Seitova, A., Al-awar, R., Mamai, A., Ackloo, S., Arrowsmith, C.H., Edwards, A.M., Halabelian, L., Structural Genomics Consortium (SGC)

To be published.

Macromolecule Content

Total Structure Weight: 72.53 kDa
Atom Count: 5,149
Modeled Residue Count: 597
Deposited Residue Count: 630
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DDB1- and CUL4-associated factor 1	A, B	315	Homo sapiens	Mutation(s): 2 Gene Names: DCAF1, KIAA0800, RIP, VPRBP EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y4B6 (Homo sapiens) Explore Q9Y4B6 Go to UniProtKB: Q9Y4B6
PHAROS: Q9Y4B6 GTEx: ENSG00000145041
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9Y4B6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1A1Q (Subject of Investigation/LOI) Query on A1A1Q Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain C [auth A] MOL2 format, chain E [auth B] MOL2 format, chain C [auth A] mmCIF format, chain E [auth B] mmCIF format, chain C [auth A]	C [auth A], E [auth B]	(4P)-N-[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]-4-(4-chloro-2-fluorophenyl)-5-[(1E)-3-oxo-3-(piperidin-1-yl)prop-1-en-1-yl]-1H-pyrrole-3-carboxamide C₂₈ H₂₆ Cl₂ F₂ N₄ O₃ WQUCFJCZXPDBNP-KDLSMAQYSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
CIT Query on CIT Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.206 (Depositor), 0.214 (DCC)
R-Value Work: 0.178 (Depositor), 0.187 (DCC)
R-Value Observed: 0.180 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.574	α = 90
b = 87.975	β = 96.94
c = 73.136	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data scaling
HKL-3000	data reduction
REFMAC	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-12-18

Deposition Author(s):

Arrowsmith, C.H.

Structural Genomics Consortium (SGC)

Funding Organization	Location	Grant Number
Other private	Canada	--

Revision History (Full details and data files)

Version 1.0: 2024-12-18
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.