Research workbench
Structure of glycosomal glyceraldehyde-3-phosphate dehydrogenase from trypanosoma cruzi in complex with the irreversible iodoacetate inhibitor
Analyse Structure of glycosomal glyceraldehyde-3-phosphate dehydrogenase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DMT
- Type
- protein
- Length
- 1,436 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glyceraldehyde-3-phosphate dehydrogenase, glycosomal
- EC
- 1.2.1.12
- UniProt
- P22513
- Ligands
- NAD
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Glyceraldehyde-3-phosphate dehydrogenase, glycosomal (EC 1.2.1.12) | protein | 359 | 31% helix, 26% strand | P22513 |
| C | Glyceraldehyde-3-phosphate dehydrogenase, glycosomal (EC 1.2.1.12) | protein | 359 | 32% helix, 26% strand | P22513 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, D, B, C
- GOL · Glycerol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 406 | 0.77 | 0.86 | 62 | empty |
| 2 | 298 | 0.72 | 0.85 | 41 | empty |
| 3 | 650 | 0.70 | 0.78 | 56 | NAD |
| 4 | 507 | 0.70 | 0.80 | 55 | NAD |
| 5 | 540 | 0.69 | 0.79 | 59 | NAD |
Interfaces
6 interfaces between chains.
- A–B · 1993 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 1993 Ų buried · 28 hydrogen bonds · protein-protein
- A–D · 1462 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 1458 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 625 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (nonstandard).
Compared structures
- 3DMT · Structure of Glycosomal Glyceraldehyde-3-Phosphate Dehydrogenase from Trypanosoma cruzi… · the same entry in another collection · chain D against D, TM-score 1.00
- P22513 · AlphaFold monomer V2.0 prediction for glyceraldehyde-3-phosphate dehydrogenase… · a predicted model of the same protein · chain D against A, TM-score 0.99
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P22513
- Elsewhere: RCSB PDB 3DMT · PDBe 3DMT · UniProt P22513
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