MolNFT v1 · #4338 · protein
Crystal structure of triose-phosphate isomerase with modified substrate binding site
1DKW · Triosephosphate isomerase: “Crystal structure of triose-phosphate isomerase with modified substrate binding site”. X-ray diffraction, 2 pockets (best druggability 0.74). MolNFT v1 #4338 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1DKW
- Type
- protein
- Length
- 472 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Triosephosphate isomerase
- EC
- 5.3.1.1
- UniProt
- P04789
- Pockets
- 2 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Triosephosphate isomerase (EC 5.3.1.1) | protein | 238 | 45% helix, 16% strand | P04789 |
| B | Triosephosphate isomerase (EC 5.3.1.1) | protein | 234 | 43% helix, 17% strand | P04789 |
Ligands and binding sites
- TBU · Tertiary-butyl alcohol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 813 | 0.74 | 0.79 | 67 | empty |
| 2 | 127 | 0.39 | 0.74 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 357 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 1DKW · Crystal structure of triose-phosphate isomerase with modified substrate binding site · the same entry in another collection · chain A against A, TM-score 1.00
- 4TIM · Crystallographic and molecular modeling studies on trypanosomal triosephosphate… · a predicted model of the same protein · chain B against A, TM-score 0.98
- 4TIM · Crystallographic and molecular modeling studies on trypanosomal triosephosphate… · a predicted model of the same protein · chain B against A, TM-score 0.98
- P04789 · AlphaFold monomer V2.0 prediction for triosephosphate isomerase, glycosomal (P04789) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 P04789
- Elsewhere: RCSB PDB 1DKW · PDBe 1DKW · UniProt P04789
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