5CI9 | pdb_00005ci9

Crystal structure of human Tob in complex with inhibitor fragment 6

• PDB DOI: https://doi.org/10.2210/pdb5CI9/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: 2.30 Å
• R-Value Free: 
  0.264 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.214 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.219 (Depositor) 

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 
• 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.
College of Life Sciences, Nankai University, Tianjin, 300071, China.
Medical Proteomics Laboratory, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan.
Cell Signal Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Onna-son, Kunigami, Okinawa, 904-0412, Japan.
Medical Proteomics Laboratory, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan. [e-mail].
State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, China. [e-mail].
College of Life Sciences, Nankai University, Tianjin, 300071, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 38.76 kDa 
• Atom Count: 993 
• Modeled Residue Count: 116 
• Deposited Residue Count: 346 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein Tob1	A	346	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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
549	B [auth A], C [auth A]	1-(propan-2-yl)-1H-benzimidazole-5-carboxylic acid C11 H12 N2 O2 SQIQIYYPWAELAC-UHFFFAOYSA-N
NA	D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.264 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.214 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.219 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.119	α = 90
b = 65.119	β = 90
c = 162.945	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-11-18 
Deposition Author(s): Bai, Y., Tashiro, S., Nagatoishi, S., Suzuki, T., Tsumoto, K., Bartlam, M., Yamamoto, T.

---

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  

• Version 1.0: 2015-11-18
  Type: Initial release
  
• Version 1.1: 2015-12-09
  Changes: Database references
• Version 1.2: 2024-03-20
  Changes: Author supporting evidence, Data collection, Database references, Derived calculations