MolNFT v1 · #53674 · protein
Crystallographic binding studies with an engineered monomeric variant of triosephosphate isomerase
2X1R · Triosephosphate isomerase, glycosomal: “Crystallographic binding studies with an engineered monomeric variant of triosephosphate isomerase”. X-ray diffraction, 2 ligands (X1R, SO4), 5 pockets (best druggability 0.80). MolNFT v1…
- PDB
- 2X1R
- Type
- protein
- Length
- 470 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Triosephosphate isomerase, glycosomal
- EC
- 5.3.1.1
- UniProt
- P04789
- Ligands
- X1R, SO4
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Triosephosphate isomerase, glycosomal (EC 5.3.1.1) | protein | 232 | 48% helix, 17% strand | P04789 |
| B | Triosephosphate isomerase, glycosomal (EC 5.3.1.1) | protein | 238 | 46% helix, 17% strand | P04789 |
Ligands and binding sites
- X1R · 3-(propylsulfonyl)propanoic acid · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1079 | 0.80 | 0.82 | 89 | empty |
| 2 | 186 | 0.54 | 0.79 | 33 | X1R |
| 3 | 81 | 0.38 | 0.77 | 19 | X1R |
| 4 | 90 | 0.34 | 0.74 | 15 | empty |
| 5 | 64 | 0.33 | 0.76 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 642 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 2X1R · Crystallographic binding studies with an engineered monomeric variant of triosephosphate… · 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 A 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 2X1R · PDBe 2X1R · UniProt P04789
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