MolNFT v1 · #12011 · protein
Structure of glycosomal glyceraldehyde-3-phosphate dehydrogenase from trypanosoma cruzi complexed with chalepin, a coumarin derivative inhibitor
1K3T: “Structure of glycosomal glyceraldehyde-3-phosphate dehydrogenase from trypanosoma cruzi complexed with…”. X-ray diffraction, 1 ligand (BRZ), 10 pockets (best druggability 0.74). MolNFT v1 #12011 on GenesisL1: 3D structure, binding…
- PDB
- 1K3T
- 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
- EC
- 1.2.1.12
- UniProt
- P22513
- Ligands
- BRZ
- Pockets
- 10 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) | protein | 359 | 32% helix, 27% strand | P22513 |
Ligands and binding sites
- BRZ · 6-(1,1-dimethylallyl)-2-(1-hydroxy-1-methylethyl)-2,3-dihydro-7H-furo[3,2-g]chromen-7-one · ligand · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1107 | 0.74 | 0.77 | 118 | BRZ |
| 2 | 403 | 0.72 | 0.83 | 44 | empty |
| 3 | 260 | 0.71 | 0.86 | 39 | empty |
| 4 | 641 | 0.68 | 0.77 | 63 | empty |
| 5 | 653 | 0.68 | 0.77 | 74 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2093 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 2065 Ų buried · 27 hydrogen bonds · protein-protein
- B–C · 1453 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 1447 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 575 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 1K3T · 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 1K3T · PDBe 1K3T · UniProt P22513
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