3B84 | pdb_00003b84

Crystal structure of the human BTB domain of the Krueppel related Zinc Finger Protein 3 (HKR3)

PDB DOI: https://doi.org/10.2210/pdb3B84/pdb

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

Deposited: 2007-10-31 Released: 2007-11-20
Deposition Author(s): Filippakopoulos, P., Bullock, A., Cooper, C., Keates, T., Salah, E., Pilka, E., Pike, A.C.W., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Weigelt, J., Knapp, S., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.74 Å
R-Value Free:
0.216 (Depositor), 0.271 (DCC)
R-Value Work:
0.186 (Depositor), 0.234 (DCC)
R-Value Observed:
0.188 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 2.2 of the entry. See complete history.

Literature

Crystal Structure of the Human BTB domain of the Krueppel related Zinc Finger Protein 3 (HKR3).

Filippakopoulos, P., Bullock, A., Cooper, C., Keates, T., Salah, E., Pilka, E., Pike, A.C.W., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Weigelt, J., Knapp, S.

To be published.

Macromolecule Content

Total Structure Weight: 13.39 kDa
Atom Count: 948
Modeled Residue Count: 113
Deposited Residue Count: 119
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Zinc finger and BTB domain-containing protein 48	A	119	Homo sapiens	Mutation(s): 0 Gene Names: ZBTB48, HKR3
UniProt & NIH Common Fund Data Resources
Find proteins for P10074 (Homo sapiens) Explore P10074 Go to UniProtKB: P10074
PHAROS: P10074 GTEx: ENSG00000204859
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P10074
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]
UNX Query on UNX Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A]	UNKNOWN ATOM OR ION X		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.74 Å
R-Value Free: 0.216 (Depositor), 0.271 (DCC)
R-Value Work: 0.186 (Depositor), 0.234 (DCC)
R-Value Observed: 0.188 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.375	α = 90
b = 50.375	β = 90
c = 86.093	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2007-11-20

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2007-11-20
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description
Version 1.3: 2023-05-31
Changes: Database references, Derived calculations
Version 2.0: 2023-06-14
Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2023-09-20
Changes: Data collection, Refinement description
Version 2.2: 2024-12-25
Changes: Advisory, Derived calculations, Structure summary