5WYI

The Yaf9 YEATS domain Recognizing H3K122suc Peptide

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Yaf9
A
165Saccharomyces cerevisiae (strain RM11-1a)Mutation(s): 3 
Find proteins for B3LNW5 (Saccharomyces cerevisiae (strain RM11-1a))
Go to UniProtKB:  B3LNW5
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Yaf9
B, C
164Saccharomyces cerevisiae (strain RM11-1a)Mutation(s): 3 
Find proteins for B3LNW5 (Saccharomyces cerevisiae (strain RM11-1a))
Go to UniProtKB:  B3LNW5
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
ILE-MET-PRO-LYS-ASP-ILE-GLN-LEU
E
8Homo sapiensMutation(s): 0 
Gene Names: H3C1, H3C2, H3C3, H3C4, H3C6, H3C7, H3C8, H3C10, H3C11, H3C12 (H3FA, HIST1H3A, H3FL, HIST1H3B, H3FC HIST1H3C, H3FB, HIST1H3D, H3FD, HIST1H3E, H3FI, HIST1H3F, H3FH, HIST1H3G, H3FK, HIST1H3H, H3FF, HIST1H3I, H3FJ, HIST1H3J)
Find proteins for P68431 (Homo sapiens)
Go to UniProtKB:  P68431
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SIN
Query on SIN
Download SDF File 
Download CCD File 
E
SUCCINIC ACID
C4 H6 O4
KDYFGRWQOYBRFD-UHFFFAOYSA-N
 Ligand Interaction
SLL
Query on SLL
Download SDF File 
Download CCD File 
C
(2S)-2-azanyl-6-[(4-hydroxy-4-oxo-butanoyl)amino]hexanoic acid
6-N-succinyl-L-lysine
C10 H18 N2 O5
ZAFOVBXOMIXMTH-ZETCQYMHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.201 
  • Space Group: P 3
Unit Cell:
Length (Å)Angle (°)
a = 136.932α = 90.00
b = 136.932β = 90.00
c = 26.168γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PHASERphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

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 

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