6UTN

Native E. coli Glyceraldehyde 3-phosphate dehydrogenase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

A Novel Substrate-Binding Site in the X-Ray Structure of an Oxidized E. coli Glyceraldehyde 3-Phosphate Dehydrogenase Elucidated by Single-Wavelength Anomalous Dispersion

Rodriguez-Hernandez, A.Romo-Arevalo, E.Rodriguez-Romero, A.

(2019) Crystals 9: 622


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glyceraldehyde-3-phosphate dehydrogenase
A, B
330Escherichia coliMutation(s): 0 
Gene Names: gapA
EC: 1.2.1.-
Find proteins for A0A0U4BD45 (Escherichia coli)
Go to UniProtKB:  A0A0U4BD45
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TRE
Query on TRE

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A, B
TREHALOSE
ALPHA-D-GLUCOPYRANOSYL-ALPHA-D-GLUCOPYRANOSIDE
C12 H22 O11
HDTRYLNUVZCQOY-LIZSDCNHSA-N
 Ligand Interaction
PO4
Query on PO4

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Download CCD File 
B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
NA
Query on NA

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Download CCD File 
A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

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Download CCD File 
A, B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
G3P
Query on G3P

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Download CCD File 
A
SN-GLYCEROL-3-PHOSPHATE
C3 H9 O6 P
AWUCVROLDVIAJX-GSVOUGTGSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
CSD
Query on CSD
A, B
L-PEPTIDE LINKINGC3 H7 N O4 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.178 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 77.673α = 90.00
b = 187.353β = 90.00
c = 121.673γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
PHASERphasing
HKL-2000data scaling
HKL-3000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-12-11
    Type: Initial release