MolNFT v1 · #23086 · protein
Comparison of the structures and the crystal contacts of trypanosomal triosephosphate isomerase in four different crystal forms
1TPF: “Comparison of the structures and the crystal contacts of trypanosomal triosephosphate isomerase in four…”. X-ray diffraction, 3 pockets (best druggability 0.44). MolNFT v1 #23086 on GenesisL1: 3D structure, binding sites and pockets…
- 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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