2YY0 | pdb_00002yy0

Crystal Structure of MS0802, c-Myc-1 binding protein domain from Homo sapiens

• PDB DOI: https://doi.org/10.2210/pdb2YY0/pdb

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


• Deposited: 2007-04-27 Released: 2008-04-29 
• Deposition Author(s): Xie, Y., Wang, H., Ihsanawati, K.T., Kishishita, S., Takemoto, C., Shirozu, M., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.289 (Depositor), 0.284 (DCC) 
• R-Value Work: 
  0.244 (Depositor), 0.243 (DCC) 
• R-Value Observed: 
  0.244 (Depositor) 

Literature

crystal structure of c-Myc-1 binding protein domain from Homo sapiens

Xie, Y., Wang, H., Ihsanawati, K.T., Kishishita, S., Takemoto, C., Murayama, K., Shirozu, M., Yokoyama, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 3  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 12-mer - A6B6 Pseudo Symmetry: Cyclic - C3  (Explore in 3D)
Pseudo Stoichiometry: Hetero 12-mer - A9B3 

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 24.47 kDa 
• Atom Count: 1,534 
• Modeled Residue Count: 181 
• Deposited Residue Count: 212 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
C-Myc-binding protein	A, B, C, D	53	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q99417 (Homo sapiens) Explore Q99417  Go to UniProtKB:  Q99417
PHAROS:  Q99417 GTEx:  ENSG00000214114

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.289 (Depositor), 0.284 (DCC) 
• R-Value Work:  0.244 (Depositor), 0.243 (DCC) 
• R-Value Observed: 0.244 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.634	α = 90
b = 59.634	β = 90
c = 194.868	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-04-29 
Deposition Author(s): Xie, Y., Wang, H., Ihsanawati, K.T., Kishishita, S., Takemoto, C., Shirozu, M., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2008-04-29
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-03-13
  Changes: Data collection, Database references
• Version 1.3: 2024-06-12
  Changes: Data collection, Database references, Structure summary
• Version 1.4: 2024-06-26
  Changes: Source and taxonomy