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 
  • R-Value Work: 0.123 
  • R-Value Observed: 0.125 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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
A, B, C, D, E, F
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

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G [auth A]
K [auth B]
O [auth C]
P [auth C]
U [auth D]
G [auth A],
K [auth B],
O [auth C],
P [auth C],
U [auth D],
Z [auth E]
SPERMINE
C10 H26 N4
PFNFFQXMRSDOHW-UHFFFAOYSA-N
HLG
Query on HLG

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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 
  • R-Value Work: 0.123 
  • R-Value Observed: 0.125 
  • 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

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Ligand Structure Quality Assessment 


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