5CI8

Crystal structure of human Tob in complex with inhibitor fragment 1

PDB DOI: https://doi.org/10.2210/pdb5CI8/pdb

Classification: TRANSCRIPTION/INHIBITOR
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2015-07-11 Released: 2015-11-18
Deposition Author(s): Bai, Y., Tashiro, S., Nagatoishi, S., Suzuki, T., Tsumoto, K., Bartlam, M., Yamamoto, T.
Funding Organization(s): Ministry of Science and Technology, Ministry of Education, Culture, Sports, Science and Technology, Japan, KAKENHI

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.33 Å
R-Value Free: 0.285
R-Value Work: 0.232
R-Value Observed: 0.238

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structural basis for inhibition of the Tob-CNOT7 interaction by a fragment screening approach

Bai, Y., Tashiro, S., Nagatoishi, S., Suzuki, T., Yan, D., Liu, R., Tsumoto, K., Bartlam, M., Yamamoto, T.

(2015) Protein Cell 6: 924-928

PubMed: 26518565 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1007/s13238-015-0225-6
Primary Citation of Related Structures:
5CI8, 5CI9

Organizational Affiliation

State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, China.

Macromolecule Content

Total Structure Weight: 38.65 kDa
Atom Count: 981
Modelled Residue Count: 117
Deposited Residue Count: 347
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein Tob1	A	347	Homo sapiens	Mutation(s): 0 Gene Names: TOB1, TOB, TROB1
UniProt & NIH Common Fund Data Resources
Find proteins for P50616 (Homo sapiens) Explore P50616 Go to UniProtKB: P50616
PHAROS: P50616 GTEx: ENSG00000141232
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P50616
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
53Y Query on 53Y Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	pyrrolo[1,2-a]quinoxalin-4(5H)-one C₁₁ H₈ N₂ O LINHQLFBBDHSEJ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.33 Å
R-Value Free: 0.285
R-Value Work: 0.232
R-Value Observed: 0.238
Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.975	α = 90
b = 64.975	β = 90
c = 163.677	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2015-11-18

Deposition Author(s):

Funding Organization	Location	Grant Number
Ministry of Science and Technology	China	2014CB560709
Ministry of Education, Culture, Sports, Science and Technology, Japan	Japan	--
KAKENHI	Japan	25121734

Revision History (Full details and data files)

Version 1.0: 2015-11-18
Type: Initial release
Version 1.1: 2015-12-09
Changes: Database references

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.