8QJM

SmNuc1 nuclease from Stenotrophomonas maltophilia in complex with cytidine-5'-monophosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.173 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Substrate preference, RNA binding and active site versatility of the Stenotrophomonas maltophilia nuclease SmNuc1, explained by a structural study

Adamkova, K.Trundova, M.Koval, T.Hustakova, B.Duskova, J.Skalova, T.Kolenko, P.Dohnalek, J.

(2024) The Febs Journal 


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
S1/P1 Nuclease
A, B
254Stenotrophomonas maltophiliaMutation(s): 0 
Gene Names: A1OC_03585
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
C5P (Subject of Investigation/LOI)
Query on C5P

Download Ideal Coordinates CCD File 
C [auth A],
P [auth B],
Q [auth B]
CYTIDINE-5'-MONOPHOSPHATE
C9 H14 N3 O8 P
IERHLVCPSMICTF-XVFCMESISA-N
1PE
Query on 1PE

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U [auth B]PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
SO4
Query on SO4

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G [auth A]
H [auth A]
I [auth A]
J [auth A]
K [auth A]
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
V [auth B],
W [auth B],
X [auth B],
Y [auth B],
Z [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
ZN (Subject of Investigation/LOI)
Query on ZN

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D [auth A]
E [auth A]
F [auth A]
R [auth B]
S [auth B]
D [auth A],
E [auth A],
F [auth A],
R [auth B],
S [auth B],
T [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
O [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.173 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.139α = 90
b = 72.805β = 105.066
c = 81.238γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Czech Science FoundationCzech Republic23-06295S
Czech Academy of SciencesCzech Republic86652036
Ministry of Education, Youth and Sports of the Czech RepublicCzech RepublicLM2023042
European Regional Development FundEuropean UnionCZ.02.1.01/0.0/0.0/18_046/0015974

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-25
    Type: Initial release