5W87 | pdb_00005w87

Crystal structure of the C-terminal lobe of the human HERC6 HECT domain

PDB DOI: https://doi.org/10.2210/pdb5W87/pdb

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

Deposited: 2017-06-21 Released: 2018-07-04
Deposition Author(s): WANG, Y., BELLESIS, A.G., ROYER, W.E., SPRATT, D.E.
Funding Organization(s): Clark University start-up funds

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.243 (Depositor), 0.244 (DCC)
R-Value Work:
0.211 (Depositor), 0.212 (DCC)
R-Value Observed:
0.213 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 5W87

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

Literature

Crystal structure of the C-terminal lobe of the human HERC6 HECT domain

WANG, Y., BELLESIS, A.G., ROYER, W.E., SPRATT, D.E.

To be published.

Macromolecule Content

Total Structure Weight: 28.86 kDa
Atom Count: 1,561
Modeled Residue Count: 191
Deposited Residue Count: 242
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable E3 ubiquitin-protein ligase HERC6	A, B	121	Homo sapiens	Mutation(s): 1 Gene Names: HERC6 EC: 2.3.2.26
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IVU3 (Homo sapiens) Explore Q8IVU3 Go to UniProtKB: Q8IVU3
PHAROS: Q8IVU3 GTEx: ENSG00000138642
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8IVU3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 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]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.243 (Depositor), 0.244 (DCC)
R-Value Work: 0.211 (Depositor), 0.212 (DCC)
R-Value Observed: 0.213 (Depositor)

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.579	α = 90
b = 74.579	β = 90
c = 114.89	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data collection
HKL-3000	data scaling
PHENIX	phasing
HKL-3000	data reduction

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2018-07-04

Deposition Author(s):

Funding Organization	Location	Grant Number
Clark University start-up funds	United States	--

Revision History (Full details and data files)

Version 1.0: 2018-07-04
Type: Initial release
Version 1.1: 2023-10-04
Changes: Data collection, Database references, Refinement description

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.