Research workbench
Refined 1.83 ångströms structure of trypanosomal triosephosphate isomerase, crystallized in the presence of 2.4 M-ammonium sulphate. a comparison with the structure of the trypanosomal triosephosphate isomerase-glycerol-3- phosphate complex
Analyse Refined 1.83 ångströms structure of trypanosomal triosephosphate isomerase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TIM
- Type
- protein
- Length
- 498 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
- Ligands
- SO4
- Pockets
- 3 · best druggability 0.45
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Triosephosphate isomerase (EC 5.3.1.1) | protein | 249 | 46% helix, 17% strand | P04789 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- DTT · 2,3-dihydroxy-1,4-dithiobutane · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 80 | 0.45 | 0.81 | 23 | SO4 |
| 2 | 125 | 0.44 | 0.77 | 32 | empty |
| 3 | 154 | 0.43 | 0.74 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 1573 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 5TIM · Refined 1.83 ångströms structure of trypanosomal triosephosphate isomerase, crystallized… · 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 1.00
- 4TIM · Crystallographic and molecular modeling studies on trypanosomal triosephosphate… · 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 P04789
- Elsewhere: RCSB PDB 5TIM · PDBe 5TIM · UniProt P04789
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