7T58 | pdb_00007t58

Crystal structure of Miz1 BTB domain

PDB DOI: https://doi.org/10.2210/pdb7T58/pdb

Classification: PROTEIN BINDING
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2021-12-11 Released: 2022-12-14
Deposition Author(s): Linhares, B.M., Cierpicki, T.
Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free:
0.231 (Depositor), 0.235 (DCC)
R-Value Work:
0.182 (Depositor), 0.187 (DCC)
R-Value Observed:
0.185 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7T58

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

Literature

Prediction of BTB domain ligandability guided by protein dynamics

Linhares, B.M., Kharchenko, V., Cierpicki, T., Jaremko, L.

To be published.

Macromolecule Content

Total Structure Weight: 25.74 kDa
Atom Count: 1,958
Modeled Residue Count: 224
Deposited Residue Count: 230
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Zinc finger and BTB domain-containing protein 17	A, B	115	Homo sapiens	Mutation(s): 0 Gene Names: ZBTB17, MIZ1, ZNF151, ZNF60
UniProt & NIH Common Fund Data Resources
Find proteins for Q13105 (Homo sapiens) Explore Q13105 Go to UniProtKB: Q13105
PHAROS: Q13105 GTEx: ENSG00000116809
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q13105
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.231 (Depositor), 0.235 (DCC)
R-Value Work: 0.182 (Depositor), 0.187 (DCC)
R-Value Observed: 0.185 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.919	α = 90
b = 115.898	β = 90
c = 64.252	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2022-12-14

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	--

Revision History (Full details and data files)

Version 1.0: 2022-12-14
Type: Initial release
Version 1.1: 2023-10-25
Changes: Data collection, 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.