8CFD

Crystal structure of S-adenosyl-L-homocysteine hydrolase from P. aeruginosa in complex with F2X-Entry library fragment A07


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.175 

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 A07

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 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

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E [auth A],
K [auth B],
Q [auth C],
Z [auth D]
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
ADE
Query on ADE

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AA [auth D],
F [auth A],
L [auth B],
R [auth C]
ADENINE
C5 H5 N5
GFFGJBXGBJISGV-UHFFFAOYSA-N
R8A (Subject of Investigation/LOI)
Query on R8A

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DA [auth D](2-aminopyridin-3-yl)methanol
C6 H8 N2 O
FEIACFYXEWBKHU-UHFFFAOYSA-N
PO4
Query on PO4

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FA [auth D]
GA [auth D]
H [auth A]
HA [auth D]
I [auth A]
FA [auth D],
GA [auth D],
H [auth A],
HA [auth D],
I [auth A],
IA [auth D],
J [auth A],
N [auth B],
O [auth B],
P [auth B],
U [auth C],
V [auth C],
W [auth C],
X [auth C],
Y [auth C]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
DMS
Query on DMS

Download Ideal Coordinates CCD File 
BA [auth D],
CA [auth D],
S [auth C]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
EA [auth D],
G [auth A],
M [auth B],
T [auth C]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.175 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 178.76α = 90
b = 105.14β = 99.71
c = 108.25γ = 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