9MK7 | pdb_00009mk7

Crystal structure of the WDR domain of WDR91 in complex with DR3634

PDB DOI: https://doi.org/10.2210/pdb9MK7/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2024-12-16 Released: 2025-02-26
Deposition Author(s): Zeng, H., Ahmad, H., Dong, A., Seitova, A., Owen, D., 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: 2.31 Å
R-Value Free:
0.238 (Depositor), 0.237 (DCC)
R-Value Work:
0.200 (Depositor), 0.206 (DCC)
R-Value Observed:
0.202 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Crystal structure of the WDR domain of WDR91 in complex with DR3634

Zeng, H., Ahmad, H., Dong, A., Seitova, A., Owen, D., Arrowsmith, C.H., Edwards, A.M., Halabelian, L., Structural Genomics Consortium (SGC)

To be published.

Macromolecule Content

Total Structure Weight: 41.47 kDa
Atom Count: 2,645
Modeled Residue Count: 337
Deposited Residue Count: 374
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
WD repeat-containing protein 91	A	374	Homo sapiens	Mutation(s): 0 Gene Names: WDR91, HSPC049
UniProt & NIH Common Fund Data Resources
Find proteins for A4D1P6 (Homo sapiens) Explore A4D1P6 Go to UniProtKB: A4D1P6
PHAROS: A4D1P6 GTEx: ENSG00000105875
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A4D1P6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1BLV (Subject of Investigation/LOI) Query on A1BLV Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	(1R)-1-({(6M)-2-(methylamino)-6-[3-(pyrrolidin-1-yl)phenyl]pyrimidin-4-yl}amino)-2,3-dihydro-1H-indene-4-carbonitrile C₂₅ H₂₆ N₆ AAOXHEZQAFYPKY-JOCHJYFZSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
UNX Query on UNX 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]	UNKNOWN ATOM OR ION X		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.31 Å
R-Value Free: 0.238 (Depositor), 0.237 (DCC)
R-Value Work: 0.200 (Depositor), 0.206 (DCC)
R-Value Observed: 0.202 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.201	α = 90
b = 132.236	β = 90
c = 118.291	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-02-26

Deposition Author(s):

Arrowsmith, C.H.

Structural Genomics Consortium (SGC)

Funding Organization	Location	Grant Number
Other private		--

Revision History (Full details and data files)

Version 1.0: 2025-02-26
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.