3PYM
Structure of GAPDH 3 from S.cerevisiae at 2.0 A resolution
- PDB DOI: https://doi.org/10.2210/pdb3PYM/pdb
- Classification: OXIDOREDUCTASE
- Organism(s): Saccharomyces cerevisiae
- Mutation(s): No 
- Deposited: 2010-12-13 Released: 2012-01-11 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.00 Å
- R-Value Free: 0.189 
- R-Value Work: 0.147 
- R-Value Observed: 0.152 
Starting Model: experimental
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This is version 1.1 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Glyceraldehyde-3-phosphate dehydrogenase 3 | 332 | Saccharomyces cerevisiae | Mutation(s): 0  EC: 1.2.1.12 | ![]() | |
UniProt | |||||
Find proteins for P00359 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P00359  Go to UniProtKB:  P00359 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P00359 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
Ligands 3 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAD Query on NAD | C [auth A], E [auth B] | NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N | |||
MRY Query on MRY | D [auth A], F [auth B] | MESO-ERYTHRITOL C4 H10 O4 UNXHWFMMPAWVPI-ZXZARUISSA-N | |||
NA Query on NA | G [auth B] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.00 Å
- R-Value Free: 0.189 
- R-Value Work: 0.147 
- R-Value Observed: 0.152 
- Space Group: C 2 2 21
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 121.834 | α = 90 |
b = 131.052 | β = 90 |
c = 96.685 | γ = 90 |
Software Name | Purpose |
---|---|
DNA | data collection |
PHASER | phasing |
PHENIX | refinement |
XDS | data reduction |
SCALA | data scaling |
Entry History 
Deposition Data
- Released Date: 2012-01-11  Deposition Author(s): Garcia-Saez, I., Kozielski, F., Job, D., Boscheron, C.
Revision History (Full details and data files)
- Version 1.0: 2012-01-11
Type: Initial release - Version 1.1: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description