8F17

Structure of the STUB1 TPR domain in complex with H204, an all-D Helicon Polypeptide

PDB DOI: https://doi.org/10.2210/pdb8F17/pdb

Classification: LIGASE
Organism(s): Homo sapiens, synthetic construct
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-11-04 Released: 2023-02-15
Deposition Author(s): Li, K., Callahan, A.J., Travaline, T.L., Tokareva, O.S., Swiecicki, J.-M., Verdine, G.L., Pentelute, B.L., McGee, J.H.
Funding Organization(s): Other private, German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.21 Å
R-Value Free: 0.254
R-Value Work: 0.216
R-Value Observed: 0.218

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.2 of the entry. See complete history.

Literature

Single-Shot Flow Synthesis of D-Proteins for Mirror-Image Phage Display

Callahan, A.J., Gandhesiri, S., Travaline, T.L., Lozano Salazar, L., Hanna, S., Lee, Y.-C., Li, K., Tokareva, O.S., Swiecicki, J.-M., Loas, A., Verdine, G.L., McGee, J.H., Pentelute, B.L.

(2023) ChemRxiv

DOI: https://doi.org/10.26434/chemrxiv-2023-x86xp

Macromolecule Content

Total Structure Weight: 34.64 kDa
Atom Count: 2,426
Modelled Residue Count: 290
Deposited Residue Count: 302
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase CHIP	A, B	134	Homo sapiens	Mutation(s): 0 Gene Names: STUB1, CHIP, PP1131 EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UNE7 (Homo sapiens) Explore Q9UNE7 Go to UniProtKB: Q9UNE7
PHAROS: Q9UNE7 GTEx: ENSG00000103266
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9UNE7
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
all-D Helicon Polypeptide H204	C, D	17	synthetic construct	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
WHL Query on WHL Download Ideal Coordinates CCD File SDF format, chain E [auth C] SDF format, chain F [auth D] MOL2 format, chain E [auth C] MOL2 format, chain F [auth D]	E [auth C], F [auth D]	N,N'-(1,4-phenylene)diacetamide C₁₀ H₁₂ N₂ O₂ KVEDKKLZCJBVNP-UHFFFAOYSA-N		Interactions Focus chain E [auth C] Focus chain F [auth D] Interactions & Density Focus chain E [auth C] Focus chain F [auth D]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain G [auth D] MOL2 format, chain G [auth D]	G [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth D] Interactions & Density Focus chain G [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.21 Å
R-Value Free: 0.254
R-Value Work: 0.216
R-Value Observed: 0.218
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.03	α = 90
b = 72.71	β = 96.31
c = 59.79	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2023-02-15

Deposition Author(s):

Funding Organization	Location	Grant Number
Other private	United States	FOG Pharmaceuticals
Other private	United States	MIT School of Science Fellowship in Cancer Research
German Research Foundation (DFG)	Germany	LE 4224/1-1

Revision History (Full details and data files)

Version 1.0: 2023-02-15
Type: Initial release
Version 2.0: 2023-09-27
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Refinement description, Structure summary
Version 2.1: 2023-10-25
Changes: Refinement description
Version 2.2: 2023-11-15
Changes: Data collection