Research workbench
Comparison of the structures and the crystal contacts of trypanosomal triosephosphate isomerase in four different crystal forms
Analyse Comparison of the structures and the crystal contacts of trypanosomal… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1TPF
- Type
- protein
- Length
- 499 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
- 3 · best druggability 0.44
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Triosephosphate isomerase (EC 5.3.1.1) | protein | 250 | 46% helix, 17% strand | P04789 |
| B | Triosephosphate isomerase (EC 5.3.1.1) | protein | 249 | 46% helix, 17% strand | P04789 |
Ligands and binding sites
- DMS · Dimethyl sulfoxide · additive · 4 copies · chains A, B
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 | 162 | 0.44 | 0.75 | 29 | empty |
| 2 | 79 | 0.40 | 0.78 | 21 | DMS |
| 3 | 77 | 0.38 | 0.78 | 21 | DMS |
Interfaces
1 interface between chains.
- A–B · 1575 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 1TPF · Comparison of the structures and the crystal contacts of trypanosomal 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 B 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 1.00
- P04789 · AlphaFold monomer V2.0 prediction for triosephosphate isomerase, glycosomal (P04789) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 1TPF · PDBe 1TPF · UniProt P04789
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