6LCB | pdb_00006lcb

Crystal structure of human Dishevelled1 PDZ domain with its inhibitor NPL3009

PDB DOI: https://doi.org/10.2210/pdb6LCB/pdb

Classification: SIGNALING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2019-11-18 Released: 2020-11-25
Deposition Author(s): Yasukochi, S., Numoto, N., Tenno, N., Tenno, T., Ito, N., Hiroaki, H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free:
0.230 (Depositor), 0.231 (DCC)
R-Value Work:
0.214 (Depositor), 0.216 (DCC)
R-Value Observed:
0.215 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Crystal structure of human Dishevelled1 PDZ domain with its inhibitor NPL3009

Yasukochi, S., Numoto, N., Tenno, N., Tenno, T., Ito, N., Hiroaki, H.

To be published.

Macromolecule Content

Total Structure Weight: 11.33 kDa
Atom Count: 774
Modeled Residue Count: 82
Deposited Residue Count: 102
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Segment polarity protein dishevelled homolog DVL-1	A	102	Homo sapiens	Mutation(s): 2 Gene Names: DVL1
UniProt & NIH Common Fund Data Resources
Find proteins for O14640 (Homo sapiens) Explore O14640 Go to UniProtKB: O14640
PHAROS: O14640 GTEx: ENSG00000107404
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O14640
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
E83 (Subject of Investigation/LOI) Query on E83 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]	2-[[3-[(2E)-2-[1,3-bis(oxidanylidene)-1-phenyl-butan-2-ylidene]hydrazinyl]phenyl]sulfonylamino]benzoic acid C₂₃ H₁₉ N₃ O₆ S SOWABNTWBBBOPH-NJNXFGOHSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
SO4 Query on SO4 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]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.230 (Depositor), 0.231 (DCC)
R-Value Work: 0.214 (Depositor), 0.216 (DCC)
R-Value Observed: 0.215 (Depositor)

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.375	α = 90
b = 85.375	β = 90
c = 46.167	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2020-11-25

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2020-11-25
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Refinement description

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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.