5TSO

CRYSTAL STRUCTURE OF GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE FROM PIG MUSCLE COMPLEXED WITH ORTHOPHENANTHROLINE AT 1.90 ANGSTROM RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.132 
  • R-Value Observed: 0.133 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Novel Enhancer Binding Site Found In Bacteria And Eukaryota But Not In Archea.

Dimova, M.Devedjiev, Y.D.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glyceraldehyde-3-phosphate dehydrogenaseA [auth P],
B [auth R],
C [auth S]
333Sus scrofaMutation(s): 0 
EC: 1.2.1.12 (PDB Primary Data), 2.6.99 (PDB Primary Data)
UniProt
Find proteins for P00355 (Sus scrofa)
Explore P00355 
Go to UniProtKB:  P00355
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00355
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download Ideal Coordinates CCD File 
F [auth P],
O [auth R],
X [auth S]
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
PHN
Query on PHN

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K [auth R],
L [auth R],
T [auth S],
U [auth S]
1,10-PHENANTHROLINE
C12 H8 N2
DGEZNRSVGBDHLK-UHFFFAOYSA-N
SO4
Query on SO4

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D [auth P]
E [auth P]
G [auth P]
H [auth P]
I [auth P]
D [auth P],
E [auth P],
G [auth P],
H [auth P],
I [auth P],
M [auth R],
N [auth R],
P [auth R],
Q [auth R],
V [auth S],
W [auth S]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
AA [auth S]
BA [auth S]
J [auth P]
R
S [auth R]
AA [auth S],
BA [auth S],
J [auth P],
R,
S [auth R],
Y [auth S],
Z [auth S]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.132 
  • R-Value Observed: 0.133 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.48α = 90
b = 133.52β = 90
c = 210.32γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
AMoREphasing
DENZOdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-05-03
    Type: Initial release
  • Version 1.1: 2017-05-31
    Changes: Atomic model
  • Version 1.2: 2018-01-31
    Changes: Database references
  • Version 1.3: 2023-10-04
    Changes: Data collection, Database references, Refinement description