3VAZ

Crystal structure of Staphylococcal GAPDH1 in a hexagonal space group


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.19 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.206 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of Staphylococcal GAPDH1 in a hexagonal space group

Roychowdhury, A.Mukherjee, S.Dutta, D.Das, A.K.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glyceraldehyde-3-phosphate dehydrogenase 1344Staphylococcus aureus subsp. aureus MRSA252Mutation(s): 0 
Gene Names: gapgapAgapA1SAR0828
EC: 1.2.1.12
UniProt
Find proteins for Q6GIL8 (Staphylococcus aureus (strain MRSA252))
Explore Q6GIL8 
Go to UniProtKB:  Q6GIL8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6GIL8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download Ideal Coordinates CCD File 
G [auth P]
K [auth R]
L [auth O]
O [auth Q]
P [auth B]
G [auth P],
K [auth R],
L [auth O],
O [auth Q],
P [auth B],
R [auth A]
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
DGY
Query on DGY

Download Ideal Coordinates CCD File 
N [auth O],
T [auth A]
(2R)-2,3-DIHYDROXYPROPANOIC ACID
C3 H6 O4
RBNPOMFGQQGHHO-UWTATZPHSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
H [auth P]
I [auth P]
J [auth P]
M [auth O]
Q [auth B]
H [auth P],
I [auth P],
J [auth P],
M [auth O],
Q [auth B],
S [auth A]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.19 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.206 
  • Space Group: P 62 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 155.389α = 90
b = 155.389β = 90
c = 317.849γ = 120
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-01-02
    Type: Initial release
  • Version 1.1: 2014-11-12
    Changes: Structure summary
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description