3DKM

Crystal structure of the HECTD1 CPH domain

• PDB DOI: https://doi.org/10.2210/pdb3DKM/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2008-06-25 Released: 2008-08-19 
• Deposition Author(s): Walker, J.R., Qiu, L., Li, Y., Bountra, C., Wolkstrom, M., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Dhe-Paganon, S., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.178 
• R-Value Work: 0.156 
• R-Value Observed: 0.157 

Starting Model: experimental

Literature

Crystal structure of the CPH domain of the E3 ubiquitin-protein ligase HECTD1.

Walker, J.R., Qiu, L., Li, Y., Bountra, C., Wolkstrom, M., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Dhe-Paganon, S.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 10.04 kDa 
• Atom Count: 742 
• Modelled Residue Count: 79 
• Deposited Residue Count: 89 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase HECTD1	A	89	Homo sapiens	Mutation(s): 1  Gene Names: HECTD1, KIAA1131 EC: 6.3.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q9ULT8 (Homo sapiens) Explore Q9ULT8  Go to UniProtKB:  Q9ULT8
PHAROS:  Q9ULT8 GTEx:  ENSG00000092148

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.178 
• R-Value Work: 0.156 
• R-Value Observed: 0.157 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.71	α = 90
b = 45.564	β = 90
c = 51.101	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
REFMAC	refinement
SBC-Collect	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-08-19 
Deposition Author(s): Walker, J.R., Qiu, L., Li, Y., Bountra, C., Wolkstrom, M., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Dhe-Paganon, S., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2008-08-19
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2023-08-30
  Changes: Data collection, Database references, Refinement description