8CFK

Crystal structure of S-adenosyl-L-homocysteine hydrolase from P. aeruginosa in complex with F2X-Entry library fragment E06


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.155 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Crystal structure of S-adenosyl-L-homocysteine hydrolase from P. aeruginosa in complex with fragment F2X-Entry E06

Malecki, P.H.Gawel, M.Stepniewska, M.Brzezinski, K.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Adenosylhomocysteinase
A, B, C, D
472Pseudomonas aeruginosa PAO1Mutation(s): 0 
Gene Names: ahcYsahHPA0432
EC: 3.3.1.1 (PDB Primary Data), 3.13.2.1 (UniProt)
UniProt
Find proteins for Q9I685 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q9I685 
Go to UniProtKB:  Q9I685
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9I685
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

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AA [auth C],
E [auth A],
IA [auth D],
Q [auth B]
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
R9V (Subject of Investigation/LOI)
Query on R9V

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CA [auth C],
H [auth A],
J [auth A],
LA [auth D],
U [auth B]
(3-endo)-8-benzyl-8-azabicyclo[3.2.1]octan-3-ol
C14 H19 N O
HCBGIBWAPOFRKI-WDNDVIMCSA-N
ADE
Query on ADE

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BA [auth C],
F [auth A],
JA [auth D],
R [auth B]
ADENINE
C5 H5 N5
GFFGJBXGBJISGV-UHFFFAOYSA-N
PO4
Query on PO4

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EA [auth C]
FA [auth C]
GA [auth C]
HA [auth C]
L [auth A]
EA [auth C],
FA [auth C],
GA [auth C],
HA [auth C],
L [auth A],
M [auth A],
N [auth A],
NA [auth D],
O [auth A],
OA [auth D],
PA [auth D],
QA [auth D],
W [auth B],
X [auth B],
Y [auth B],
Z [auth B]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL
Query on GOL

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I [auth A],
KA [auth D],
P [auth B],
S [auth B],
T [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS
Query on DMS

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G [auth A]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
K
Query on K

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DA [auth C],
K [auth A],
MA [auth D],
V [auth B]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.155 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.57α = 90
b = 132.39β = 101.93
c = 98.85γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling
XDSdata reduction
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Polish National Science CentrePolandSONATA BIS 2018/30/E/NZ1/00729

Revision History  (Full details and data files)

  • Version 1.0: 2024-02-21
    Type: Initial release