6IM5 | pdb_00006im5

YAP-binding domain of human TEAD1

• PDB DOI: https://doi.org/10.2210/pdb6IM5/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-10-22 Released: 2019-02-06 
• Deposition Author(s): Mo, Y., Lee, H.S., Kim, S.J., Ku, B.
• Funding Organization(s): National Research Foundation (Korea), Ministry of Science, ICT and Future Planning

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.230 (Depositor), 0.231 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.195 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of the YAP-binding Domain of Human TEAD1

Mo, Y., Lee, H.S., Lee, C.H., Lim, H.J., Park, S.J., Shin, H.-C., Kim, C.-H., Kim, S.J., Ku, B.

(2019) Bull Korean Chem Soc 40: 74-77

• DOI: https://doi.org/10.1002/bkcs.11639

Biological Assembly 1  

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

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

Biological Assembly Evidence: light scattering

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 53.64 kDa 
• Atom Count: 3,899 
• Modeled Residue Count: 432 
• Deposited Residue Count: 466 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional enhancer factor TEF-1	A, B	233	Homo sapiens	Mutation(s): 0  Gene Names: TEAD1, TCF13, TEF1
UniProt & NIH Common Fund Data Resources
Find proteins for P28347 (Homo sapiens) Explore P28347  Go to UniProtKB:  P28347
PHAROS:  P28347 GTEx:  ENSG00000187079

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	C [auth A], D [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.230 (Depositor), 0.231 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.195 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.537	α = 90
b = 89.356	β = 90
c = 135.569	γ = 90

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: 2019-02-06 
Deposition Author(s): Mo, Y., Lee, H.S., Kim, S.J., Ku, B.

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Funding Organization	Location	Grant Number
National Research Foundation (Korea)	Korea, Republic Of	2015M3A9B5030308
Ministry of Science, ICT and Future Planning	Korea, Republic Of	Creative Research
Ministry of Science, ICT and Future Planning	Korea, Republic Of	Disease Target Structure Research
Ministry of Science, ICT and Future Planning	Korea, Republic Of	KK1803

Revision History  

• Version 1.0: 2019-02-06
  Type: Initial release
  
• Version 1.1: 2019-10-30
  Changes: Data collection
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Refinement description