8F17 | pdb_00008f17

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 (Depositor), 0.255 (DCC)
R-Value Work:
0.216 (Depositor), 0.220 (DCC)
R-Value Observed:
0.218 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.3 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
Modeled Residue Count: 290
Deposited Residue Count: 302
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	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 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 F [auth D] SDF format, chain E [auth C] MOL2 format, chain F [auth D] MOL2 format, chain E [auth C] mmCIF format, chain F [auth D] mmCIF format, chain E [auth C]	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] mmCIF 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]

Modified Residues 11 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
DAL Query on DAL	C, D	D-PEPTIDE LINKING	C₃ H₇ N O₂		--
DAS Query on DAS	C, D	D-PEPTIDE LINKING	C₄ H₇ N O₄		--
DCY Query on DCY	C, D	D-PEPTIDE LINKING	C₃ H₇ N O₂ S		--
DHI Query on DHI	C, D	D-PEPTIDE LINKING	C₆ H₁₀ N₃ O₂		--
DIL Query on DIL	C, D	D-PEPTIDE LINKING	C₆ H₁₃ N O₂		--
DLE Query on DLE	C, D	D-PEPTIDE LINKING	C₆ H₁₃ N O₂		--
DPR Query on DPR	C, D	D-PEPTIDE LINKING	C₅ H₉ N O₂		--
DSN Query on DSN	C, D	D-PEPTIDE LINKING	C₃ H₇ N O₃		--
DTR Query on DTR	C, D	D-PEPTIDE LINKING	C₁₁ H₁₂ N₂ O₂		--
DTY Query on DTY	C, D	D-PEPTIDE LINKING	C₉ H₁₁ N O₃		--
DVA Query on DVA	C, D	D-PEPTIDE LINKING	C₅ H₁₁ N O₂		--

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.21 Å
R-Value Free: 0.254 (Depositor), 0.255 (DCC)
R-Value Work: 0.216 (Depositor), 0.220 (DCC)
R-Value Observed: 0.218 (Depositor)

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

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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 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
Version 2.3: 2024-11-06
Changes: Structure summary