5WYI

The Yaf9 YEATS domain Recognizing H3K122suc Peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

The Yaf9 YEATS domain Recognizing H3K122suc Peptide

Wang, Y.Hao, Q.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Yaf9A165Saccharomyces cerevisiae RM11-1aMutation(s): 3 
Gene Names: SCRG_03242YAF9
UniProt
Find proteins for B3LNW5 (Saccharomyces cerevisiae (strain RM11-1a))
Explore B3LNW5 
Go to UniProtKB:  B3LNW5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB3LNW5
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Yaf9B, C164Saccharomyces cerevisiae RM11-1aMutation(s): 3 
Gene Names: SCRG_03242YAF9
UniProt
Find proteins for B3LNW5 (Saccharomyces cerevisiae (strain RM11-1a))
Explore B3LNW5 
Go to UniProtKB:  B3LNW5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB3LNW5
Protein Feature View
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
ILE-MET-PRO-LYS-ASP-ILE-GLN-LEUD [auth E]8Homo sapiensMutation(s): 0 
Gene Names: 
UniProt & NIH Common Fund Data Resources
Find proteins for P68431 (Homo sapiens)
Explore P68431 
Go to UniProtKB:  P68431
PHAROS:  P68431
Entity Groups  
UniProt GroupP68431
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SLL
Query on SLL

Download Ideal Coordinates CCD File 
E [auth C](2S)-2-azanyl-6-[(4-hydroxy-4-oxo-butanoyl)amino]hexanoic acid
C10 H18 N2 O5
ZAFOVBXOMIXMTH-ZETCQYMHSA-N
 Ligand Interaction
SIN
Query on SIN

Download Ideal Coordinates CCD File 
F [auth E]SUCCINIC ACID
C4 H6 O4
KDYFGRWQOYBRFD-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 
  • Space Group: P 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 136.932α = 90
b = 136.932β = 90
c = 26.168γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-01-13 
  • Released Date: 2018-01-17 
  • Deposition Author(s): Wang, Y., Hao, Q.

Funding OrganizationLocationGrant Number
HK-RGCHong KongC7037-14G

Revision History  (Full details and data files)

  • Version 1.0: 2018-01-17
    Type: Initial release