5M6D

Streptococcus pneumoniae Glyceraldehyde-3-Phosphate Dehydrogenase (SpGAPDH) crystal structure


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.215
  • R-Value Work: 0.195

Literature

Macromolecules
Sequence Display for 5M6D

Classification: OXIDOREDUCTASE

Total Structure Weight: 77388.00

Macromolecule Entities
Molecule Chains Length Organism Details
Glyceraldehyde-3-phosphate dehydrogenase A, B 355 Streptococcus pneumoniae EC#: 1.2.1 IUBMB
Details: The active site cystein is oxidized, this why there seems to be a mismatch between sequence and coordinates, but this is not the case
Gene Name(s): gapdh gap gapA gapA_3 A4260_06920 ERS003549_02320 ERS019166_02194 ERS019420_02001 ERS019499_02096 ERS020135_02122 ERS020141_02006 ERS020142_02114 ERS020143_02138 ERS020145_02042 ERS020146_02116 ERS020147_02108 ERS020151_01255 ERS020155_02130 ERS020157_02177 ERS020178_05802 ERS020520_01871 ERS020522_01677 ERS020523_02061 ERS020524_02058 ERS020526_04928 ERS020526_06565 ERS020527_02055 ERS020531_01991 ERS020539_02263 ERS020541_02011 ERS020726_03159 ERS020822_04318 ERS020831_02217 ERS020873_02164 ERS021047_02054 ERS021354_07537 ERS021360_02109 ERS021447_07389 ERS022199_02215 ERS022232_07453 ERS096208_02293 ERS232497_02152 ERS367628_02144 ERS394170_00349 ERS409165_02221 ERS409372_02114 ERS409444_01606 ERS455085_02183 ERS455152_02113 ERS515225_02154 SpnNT_02067
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
GOL
Query on GOL

B GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ACY
Query on ACY

A, B ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A, B CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
CSU
Query on CSU
A, B L-PEPTIDE LINKING C3 H7 N O5 S2 CYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.215
  • R-Value Work: 0.195
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 81.04 α = 90.00
b = 130.24 β = 119.64
c = 79.84 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2016-10-25
  • Released Date: 2017-01-11
  • Deposition author(s): Gaboriaud, C., Moreau, C.P., Di Guilmi, A.M.

Revision History

  • Version 1_0: 2017-01-11

    Type: Initial release

  • Version 1_1: 2017-02-22

    Type: Database references

  • Version 1_2: 2017-09-06

    Type: Advisory, Author supporting evidence