6XRS

Crystal structure of a GTP-binding protein EngA (Der homolog) from Neisseria gonorrhoeae bound to GDP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 

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 a GTP-binding protein EngA (Der homolog) from Neisseria gonorrhoeae bound to GDP

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

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GTPase Der
A, B, C, D
458Neisseria gonorrhoeae NCCP11945Mutation(s): 0 
Gene Names: derengANGK_0592
UniProt
Find proteins for B4RKD2 (Neisseria gonorrhoeae (strain NCCP11945))
Explore B4RKD2 
Go to UniProtKB:  B4RKD2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB4RKD2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GDP (Subject of Investigation/LOI)
Query on GDP

Download Ideal Coordinates CCD File 
E [auth A]
H [auth B]
I [auth B]
L [auth C]
M [auth C]
E [auth A],
H [auth B],
I [auth B],
L [auth C],
M [auth C],
Q [auth D]
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
IOD
Query on IOD

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B],
N [auth C],
R [auth D]
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
CL
Query on CL

Download Ideal Coordinates CCD File 
G [auth A],
K [auth B],
O [auth C],
P [auth C],
S [auth D]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 138.16α = 90
b = 139.64β = 90
c = 127γ = 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 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-23
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Database references, Refinement description