4MY0

Crystal Structure of GCN5-related N-acetyltransferase from Kribbella flavida


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.202 (Depositor), 0.203 (DCC) 
  • R-Value Work: 
    0.166 (Depositor), 0.168 (DCC) 
  • R-Value Observed: 
    0.168 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted AC8Click on this verticalbar to view detailsBest fitted ACOClick on this verticalbar to view details

This is version 1.1 of the entry. See complete history


Literature

Crystal Structure of GCN5-related N-acetyltransferase from Kribbella flavida

Kim, Y.Mack, J.Endres, M.Joachimiak, A.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GCN5-related N-acetyltransferase
A, B, C, D, E
392Kribbella flavida DSM 17836Mutation(s): 0 
Gene Names: Kfla_4406
UniProt
Find proteins for D2PVF8 (Kribbella flavida (strain DSM 17836 / JCM 10339 / NBRC 14399))
Explore D2PVF8 
Go to UniProtKB:  D2PVF8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD2PVF8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AC8
Query on AC8

Download Ideal Coordinates CCD File 
L [auth C][(2R,3R,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-bis(phosphonooxy)tetrahydrofuran-2-yl]methyl (3R)-3-hydroxy-2,2-dimethyl-4-oxo-4-({3-oxo-3-[(2-sulfanylethyl)amino]propyl}amino)butyl dihydrogen diphosphate
C21 H37 N7 O19 P4 S
SAXULFDJRFDTDN-IBOSZNHHSA-N
ACO
Query on ACO

Download Ideal Coordinates CCD File 
G [auth A],
J [auth B],
N [auth D],
P [auth E],
S [auth F]
ACETYL COENZYME *A
C23 H38 N7 O17 P3 S
ZSLZBFCDCINBPY-ZSJPKINUSA-N
TRS
Query on TRS

Download Ideal Coordinates CCD File 
H [auth A]
K [auth B]
M [auth C]
O [auth D]
Q [auth E]
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
GOL
Query on GOL

Download Ideal Coordinates CCD File 
I [auth A],
R [auth E]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.202 (Depositor), 0.203 (DCC) 
  • R-Value Work:  0.166 (Depositor), 0.168 (DCC) 
  • R-Value Observed: 0.168 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.138α = 90
b = 166.518β = 90
c = 183.613γ = 90
Software Package:
Software NamePurpose
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
SHELXDphasing
MLPHAREphasing
DMmodel building
RESOLVEmodel building
Cootmodel building
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted AC8Click on this verticalbar to view detailsBest fitted ACOClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-11-06
    Type: Initial release
  • Version 1.1: 2024-10-09
    Changes: Data collection, Database references, Derived calculations, Structure summary