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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free: 
  0.239 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Starting Model: experimental

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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

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

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
NA	D [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free:  0.239 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.200 (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

Entry History & Funding Information

Deposition Data

• Released Date: 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.

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Funding Organization	Location	Grant Number
Innovative Medicines Initiative	United Kingdom	875510

Revision History  

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