Research workbench
Structure of glycosomal glyceraldehyde-3-phosphate dehydrogenase from trypanosoma cruzi in complex with the irreversible iodoacetamide 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
- 3IDS
- 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
- ACM, NAD
- Pockets
- 6 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, D, A, B | Glyceraldehyde-3-phosphate dehydrogenase, glycosomal (EC 1.2.1.12) | protein | 359 | 31% helix, 26% strand | P22513 |
Ligands and binding sites
- ACM · Acetamide · ligand · 3 copies · chains C, A, B
- NAD · Nicotinamide-adenine-dinucleotide · ligand · chains D, A
- GOL · Glycerol · additive · 6 copies · chains C, A, D, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1001 | 0.83 | 0.83 | 120 | empty |
| 2 | 544 | 0.69 | 0.79 | 57 | NAD |
| 3 | 693 | 0.69 | 0.77 | 74 | ACM |
| 4 | 603 | 0.68 | 0.77 | 63 | ACM |
| 5 | 417 | 0.65 | 0.78 | 67 | ACM |
Interfaces
6 interfaces between chains.
- C–D · 2060 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 2056 Ų buried · 27 hydrogen bonds · protein-protein
- C–B · 1451 Ų buried · 18 hydrogen bonds · protein-protein
- D–A · 1442 Ų buried · 21 hydrogen bonds · protein-protein
- C–A · 538 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 3IDS · Structure of Glycosomal Glyceraldehyde-3-Phosphate Dehydrogenase from Trypanosoma cruzi… · the same entry in another collection · chain B against B, 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 1.00
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 3IDS · PDBe 3IDS · UniProt P22513
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