7S5E

Crystal structure of a guanylate kinase from Stenotrophomonas maltophilia K279a with heterogeneous ligand states of GMP/ADP, GMP/-, GDP/-, and GMP/ATPgS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.227 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Crystal structure of a guanylate kinase from Stenotrophomonas maltophilia K279c with heterogeneous ligand states of GMP/ADP, GMP/-, GDP/-, and GMP/ATPgS.

Edwards, T.E.Horanyi, P.S.Abendroth, J.Lorimer, D.D.Seattle Structural Genomics Center for Infectious Disease (SSGCID)

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Guanylate kinaseA, B, C, D, E, F, G, H229Stenotrophomonas maltophilia K279aMutation(s): 0 
Gene Names: gmkSmlt3842
EC: 2.7.4.8
UniProt
Find proteins for B2FT06 (Stenotrophomonas maltophilia (strain K279a))
Explore B2FT06 
Go to UniProtKB:  B2FT06
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AGS (Subject of Investigation/LOI)
Query on AGS

Download Ideal Coordinates CCD File 
N [auth D], T [auth H]PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
C10 H16 N5 O12 P3 S
NLTUCYMLOPLUHL-KQYNXXCUSA-N
 Ligand Interaction
GDP (Subject of Investigation/LOI)
Query on GDP

Download Ideal Coordinates CCD File 
L [auth C], R [auth G]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
ADP (Subject of Investigation/LOI)
Query on ADP

Download Ideal Coordinates CCD File 
J [auth A], P [auth E]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
5GP (Subject of Investigation/LOI)
Query on 5GP

Download Ideal Coordinates CCD File 
I [auth A], K [auth B], M [auth D], O [auth E], Q [auth F], S [auth H]GUANOSINE-5'-MONOPHOSPHATE
C10 H14 N5 O8 P
RQFCJASXJCIDSX-UUOKFMHZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.16α = 90
b = 100.53β = 95.21
c = 92.25γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2021-09-22
    Type: Initial release