7QZQ | pdb_00007qzq

Crystal structure of the kelch domain of human KBTBD12

PDB DOI: https://doi.org/10.2210/pdb7QZQ/pdb

Classification: LIGASE
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda multiple nucleopolyhedrovirus
Mutation(s): No

Deposited: 2022-01-31 Released: 2022-05-04
Deposition Author(s): Manning, C.E., Chen, Z., Chen, X., Bradshaw, W.J., Bakshi, S., Mckinley, G., Chalk, R., Burgess-Brown, N., von Delft, F., Bullock, A.N.
Funding Organization(s): Innovative Medicines Initiative

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.88 Å
R-Value Free:
0.239 (Depositor), 0.199 (DCC)
R-Value Work:
0.195 (Depositor), 0.197 (DCC)
R-Value Observed:
0.197 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of the kelch domain of human KBTBD12

Manning, C.E., Chen, Z., Chen, X., Bakshi, S., Mckinley, G., Chalk, R., Burgess-Brown, N., von Delft, F., Bullock, A.N.

To be published.

Macromolecule Content

Total Structure Weight: 81.81 kDa
Atom Count: 5,761
Modeled Residue Count: 686
Deposited Residue Count: 724
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Kelch repeat and BTB domain-containing protein 12	A, B	362	Homo sapiens	Mutation(s): 0 Gene Names: KBTBD12, KLHDC6
UniProt & NIH Common Fund Data Resources
Find proteins for Q3ZCT8 (Homo sapiens) Explore Q3ZCT8 Go to UniProtKB: Q3ZCT8
PHAROS: Q3ZCT8 GTEx: ENSG00000187715
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q3ZCT8
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 C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
NA Query on NA 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]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.88 Å
R-Value Free: 0.239 (Depositor), 0.199 (DCC)
R-Value Work: 0.195 (Depositor), 0.197 (DCC)
R-Value Observed: 0.197 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.379	α = 90
b = 55.078	β = 108.67
c = 95.164	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-05-04

Deposition Author(s):

Funding Organization	Location	Grant Number
Innovative Medicines Initiative	United Kingdom	875510

Revision History (Full details and data files)

Version 1.0: 2022-05-04
Type: Initial release
Version 1.1: 2024-01-31
Changes: Data collection, Database references, Refinement description, Structure summary