5WYI | pdb_00005wyi

The Yaf9 YEATS domain Recognizing H3K122suc Peptide

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.226 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.201 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.203 (Depositor) 

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Ligand Structure Quality Assessment 


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


Literature

The Yaf9 YEATS domain Recognizing H3K122suc Peptide

Wang, Y., Hao, Q.

To be published.

Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Yaf9165Saccharomyces cerevisiae RM11-1aMutation(s): 3 
Gene Names: SCRG_03242
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
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Yaf9
B, C
164Saccharomyces cerevisiae RM11-1aMutation(s): 3 
Gene Names: SCRG_03242
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
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ILE-MET-PRO-LYS-ASP-ILE-GLN-LEUD [auth E]8Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P68431 (Homo sapiens)
Explore P68431 
Go to UniProtKB:  P68431
PHAROS:  P68431
GTEx:  ENSG00000197409 ENSG00000197153 ENSG00000278828 ENSG00000275714 ENSG00000273983 ENSG00000274750 ENSG00000275379 ENSG00000277775 
Entity Groups  
UniProt GroupP68431
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / 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
SIN
Query on SIN
Download Ideal Coordinates CCD File 
F [auth E]SUCCINIC ACID
C4 H6 O4
KDYFGRWQOYBRFD-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.226 (Depositor), 0.230 (DCC) 
  • R-Value Work:  0.201 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.203 (Depositor) 
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

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
HK-RGCHong KongC7037-14G

Revision History  (Full details and data files)

  • Version 1.0: 2018-01-17
    Type: Initial release
  • Version 1.1: 2025-04-09
    Changes: Data collection, Database references, Structure summary