6E1X

Crystal structure of product-bound complex of spermidine/spermine N-acetyltransferase SpeG


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 
    0.151 (Depositor), 0.150 (DCC) 
  • R-Value Work: 
    0.123 (Depositor), 0.120 (DCC) 
  • R-Value Observed: 
    0.125 (Depositor) 

Starting Model: experimental
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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 SP5Click on this verticalbar to view detailsBest fitted SPMClick on this verticalbar to view detailsBest fitted HLGClick on this verticalbar to view details

This is version 1.1 of the entry. See complete history


Literature

Crystal structure of product-bound complex of spermidine/spermine N-acetyltransferase SpeG from Vibrio cholerae.

Filippova, E.V.Kiryukhina, O.Anderson, W.F.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Spermidine N(1)-acetyltransferase
A, B, C, D, E
176Vibrio cholerae O1 biovar El Tor str. N16961Mutation(s): 0 
Gene Names: speGVC_A0947
EC: 2.3.1.57
UniProt
Find proteins for Q9KL03 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961))
Explore Q9KL03 
Go to UniProtKB:  Q9KL03
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9KL03
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SP5
Query on SP5

Download Ideal Coordinates CCD File 
H [auth A],
L [auth B],
V [auth D]
N-[3-({4-[(3-aminopropyl)amino]butyl}amino)propyl]acetamide
C12 H28 N4 O
GUNURVWAJRRUAV-UHFFFAOYSA-N
SPM
Query on SPM

Download Ideal Coordinates CCD File 
G [auth A]
K [auth B]
O [auth C]
P [auth C]
U [auth D]
SPERMINE
C10 H26 N4
PFNFFQXMRSDOHW-UHFFFAOYSA-N
HLG
Query on HLG

Download Ideal Coordinates CCD File 
Q [auth C]N-{3-[(4-aminobutyl)amino]propyl}acetamide
C9 H21 N3 O
MQTAVJHICJWXBR-UHFFFAOYSA-N
TRS
Query on TRS

Download Ideal Coordinates CCD File 
J [auth A],
N [auth B]
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
MPD
Query on MPD

Download Ideal Coordinates CCD File 
M [auth B],
T [auth C],
Y [auth D]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
MRD
Query on MRD

Download Ideal Coordinates CCD File 
I [auth A],
R [auth C],
S [auth C],
W [auth D],
X [auth D]
(4R)-2-METHYLPENTANE-2,4-DIOL
C6 H14 O2
SVTBMSDMJJWYQN-RXMQYKEDSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free:  0.151 (Depositor), 0.150 (DCC) 
  • R-Value Work:  0.123 (Depositor), 0.120 (DCC) 
  • R-Value Observed: 0.125 (Depositor) 
Space Group: C 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 185.979α = 90
b = 186.502β = 90
c = 73.722γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
BLU-MAXdata collection
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
Cootmodel building

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 SP5Click on this verticalbar to view detailsBest fitted SPMClick on this verticalbar to view detailsBest fitted HLGClick on this verticalbar to view details

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-10
    Type: Initial release
  • Version 1.1: 2023-10-11
    Changes: Data collection, Database references, Refinement description