Download MendeleyKinetic and Crystallographic Studies on Glyceraldehyde-3-Phosphate Dehydrogenase from Trypanosoma cruzi in Complex with Iodoacetate.
Guido, R.V.C., Balliano, T.L., Andricopulo, A.D., Oliva, G.(2009) Letters In Drug Design & Discovery 6: 210-214
3DMT
Structure of Glycosomal Glyceraldehyde-3-Phosphate Dehydrogenase from Trypanosoma cruzi in complex with the irreversible iodoacetate inhibitor
- PDB DOI: https://doi.org/10.2210/pdb3DMT/pdb
- Classification: OXIDOREDUCTASE
- Organism(s): Trypanosoma cruzi
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2008-07-01 Released: 2008-10-21
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.30 Å
- R-Value Free: 0.252
- R-Value Work: 0.186
- R-Value Observed: 0.190
This is version 1.3 of the entry. See complete history.
Literature
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Glyceraldehyde-3-phosphate dehydrogenase, glycosomal | 359 | Trypanosoma cruzi | Mutation(s): 0 Gene Names: TcGAP EC: 1.2.1.12 |  | |
UniProt | |||||
Find proteins for P22513 (Trypanosoma cruzi) Explore P22513 Go to UniProtKB: P22513 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P22513 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Glyceraldehyde-3-phosphate dehydrogenase, glycosomal | 359 | Trypanosoma cruzi | Mutation(s): 0 Gene Names: TcGAP EC: 1.2.1.12 |  | |
UniProt | |||||
Find proteins for P22513 (Trypanosoma cruzi) Explore P22513 Go to UniProtKB: P22513 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P22513 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| NAD Query on NAD | E [auth A], F [auth B], G [auth C], I [auth D] | NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N |  | ||
| GOL Query on GOL | H [auth C] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| CCS Query on CCS | C | L-PEPTIDE LINKING | C5 H9 N O4 S |  | CYS |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.30 Å
- R-Value Free: 0.252
- R-Value Work: 0.186
- R-Value Observed: 0.190
- Space Group: P 1 21 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 78.755 | α = 90 |
| b = 83.713 | β = 96.44 |
| c = 105.611 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| MAR345dtb | data collection |
| MOSFLM | data reduction |
| SCALA | data scaling |
| MOLREP | phasing |
| PHENIX | refinement |
Entry History
Deposition Data
- Released Date: 2008-10-21 Deposition Author(s): Guido, R.V.C., Balliano, T.L., Andricopulo, A.D., Oliva, G.
Revision History (Full details and data files)
- Version 1.0: 2008-10-21
Type: Initial release - Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance - Version 1.2: 2019-07-24
Changes: Data collection, Derived calculations, Refinement description - Version 1.3: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description
