Research workbench
Crystal structure of leishmanial E65Q-tim complexed with S-glycidol phosphate
Analyse Crystal structure of leishmanial E65Q-tim complexed with S-glycidol phosphate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Y61
- Type
- protein
- Length
- 249 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Triosephosphate isomerase synonym triose-phosphate isomerase, tim
- EC
- 5.3.1.1
- UniProt
- P48499
- Ligands
- 1GP, G3P
- Pockets
- 1 · best druggability 0.43
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Triosephosphate isomerase synonym triose-phosphate isomerase, tim (EC 5.3.1.1) | protein | 249 | 46% helix, 16% strand | P48499 |
Ligands and binding sites
- 1GP · Sn-glycerol-1-phosphate · ligand · chains A
- G3P · Sn-glycerol-3-phosphate · ligand · chains A
- GOL · Glycerol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 92 | 0.43 | 0.79 | 15 | empty |
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 2Y61 · Crystal structure of Leishmanial E65Q-TIM complexed with S-Glycidol phosphate · the same entry in another collection · chain A against A, TM-score 1.00
- P48499 · AlphaFold monomer V2.0 prediction for triosephosphate isomerase (P48499) · a predicted model of the same protein · chain A 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 P48499
- Elsewhere: RCSB PDB 2Y61 · PDBe 2Y61 · UniProt P48499
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