MolNFT v1 · #19888 · protein
Crystal structure of trypanosoma cruzi glyceraldehyde-3- phosphate dehydrogenase complexed with an analogue of 1,3- bisphospho-D- glyceric acid
1QXS · Glyceraldehyde 3-phosphate dehydrogenase, glycosomal: “Crystal structure of trypanosoma cruzi glyceraldehyde-3- phosphate dehydrogenase complexed with an analogue…”. X-ray diffraction, 2 ligands (NAD, S70), 5 pockets (best…
- PDB
- 1QXS
- 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, S70
- Pockets
- 5 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 25% 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, 25% strand | P22513 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains C, B, D, A
- S70 · 3-hydroxy-2-oxo-4-phophonoxy- butyl)-phosphonic acid · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 995 | 0.83 | 0.84 | 114 | empty |
| 2 | 996 | 0.77 | 0.79 | 126 | NAD, S70 |
| 3 | 639 | 0.67 | 0.76 | 68 | NAD |
| 4 | 574 | 0.66 | 0.77 | 63 | NAD |
| 5 | 51 | 0.26 | 0.73 | 13 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2015 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 2004 Ų buried · 27 hydrogen bonds · protein-protein
- D–A · 1444 Ų buried · 23 hydrogen bonds · protein-protein
- C–B · 1421 Ų buried · 16 hydrogen bonds · protein-protein
- D–B · 593 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 1QXS · CRYSTAL STRUCTURE OF Trypanosoma cruzi GLYCERALDEHYDE-3- PHOSPHATE DEHYDROGENASE… · 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 1QXS · PDBe 1QXS · UniProt P22513
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