8F15 | pdb_00008f15

Structure of the STUB1 TPR domain in complex with H202, an all-D Helicon Polypeptide

PDB DOI: https://doi.org/10.2210/pdb8F15/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: 1.73 Å
R-Value Free:
0.210 (Depositor), 0.212 (DCC)
R-Value Work:
0.180 (Depositor), 0.182 (DCC)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 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: 52.75 kDa
Atom Count: 4,113
Modeled Residue Count: 445
Deposited Residue Count: 453
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase CHIP	A, B, C	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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 H202	D, E, F	17	synthetic construct	Mutation(s): 0

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 N [auth D] SDF format, chain O [auth E] SDF format, chain P [auth F] MOL2 format, chain N [auth D] MOL2 format, chain O [auth E] MOL2 format, chain P [auth F] mmCIF format, chain N [auth D] mmCIF format, chain O [auth E] mmCIF format, chain P [auth F]	N [auth D], O [auth E], P [auth F]	N,N'-(1,4-phenylene)diacetamide C₁₀ H₁₂ N₂ O₂ KVEDKKLZCJBVNP-UHFFFAOYSA-N		Interactions Focus chain N [auth D] Focus chain O [auth E] Focus chain P [auth F] Interactions & Density Focus chain N [auth D] Focus chain O [auth E] Focus chain P [auth F]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth B] SDF format, chain K [auth B] SDF format, chain L [auth C] SDF format, chain M [auth C] SDF format, chain J [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth C] MOL2 format, chain M [auth C] MOL2 format, chain J [auth B] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth C] mmCIF format, chain M [auth C] mmCIF format, chain J [auth B]	G [auth A] H [auth A] I [auth B] J [auth B] K [auth B] G [auth A], H [auth A], I [auth B], J [auth B], K [auth B], L [auth C], M [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth C] Focus chain M [auth C] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth C] Focus chain M [auth C]

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002515 Query on PRD_002515	D, E, F	all-D Helicon Polypeptide FP40918	Peptide-like / Substrate analog		Interactions Focus chain D Focus chain E Focus chain F Interactions & Density Focus chain D Focus chain E Focus chain F

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.73 Å
R-Value Free: 0.210 (Depositor), 0.212 (DCC)
R-Value Work: 0.180 (Depositor), 0.182 (DCC)

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.56	α = 90
b = 50.56	β = 90
c = 199.85	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

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 1.1: 2023-10-25
Changes: Data collection, Refinement description
Version 1.2: 2023-11-15
Changes: Data collection
Version 1.3: 2024-10-09
Changes: Structure summary
Version 1.4: 2024-10-16
Changes: Database references

8F15 | pdb_00008f15

Structure of the STUB1 TPR domain in complex with H202, an all-D Helicon Polypeptide

Literature

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

Biological Assembly 1

Biological Assembly 2

Biological Assembly 3

Macromolecules

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Entity ID: 2