2VKP | pdb_00002vkp

Crystal structure of BTB domain from BTBD6

PDB DOI: https://doi.org/10.2210/pdb2VKP/pdb

Classification: PROTEIN BINDING
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2007-12-21 Released: 2008-02-12
Deposition Author(s): Cooper, C.D.O., Pike, A.C.W., Salah, E., Filippakopoulos, P., Bunkoczi, G., Elkins, J.M., von Delft, F., Gileadi, O., Edwards, A., Weigelt, J., Arrowsmith, C.H., Knapp, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.234 (Depositor), 0.237 (DCC)
R-Value Work:
0.194 (Depositor), 0.198 (DCC)
R-Value Observed:
0.196 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Crystal Structure of Btb Domain from Btbd6

Cooper, C.D.O., Pike, A.C.W., Salah, E., Filippakopoulos, P., Bunkoczi, G., Elkins, J.M., von Delft, F., Gileadi, O., Edwards, A., Weigelt, J., Arrowsmith, C.H., Knapp, S.

To be published.

Macromolecule Content

Total Structure Weight: 24.42 kDa
Atom Count: 1,808
Modeled Residue Count: 212
Deposited Residue Count: 218
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BTB/POZ DOMAIN-CONTAINING PROTEIN 6	A, B	109	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q96KE9 (Homo sapiens) Explore Q96KE9 Go to UniProtKB: Q96KE9
PHAROS: Q96KE9 GTEx: ENSG00000184887
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q96KE9
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 D [auth B] MOL2 format, chain D [auth B] mmCIF format, chain D [auth B]	D [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.234 (Depositor), 0.237 (DCC)
R-Value Work: 0.194 (Depositor), 0.198 (DCC)
R-Value Observed: 0.196 (Depositor)

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.135	α = 90
b = 58.135	β = 90
c = 332.456	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
SHELXDE	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2008-02-12

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-02-12
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2013-03-06
Changes: Data collection, Database references, Derived calculations, Other
Version 1.3: 2017-12-13
Changes: Database references, Source and taxonomy
Version 1.4: 2024-11-20
Changes: Data collection, Database references, Derived calculations, Other, Structure summary