MolNFT v1 · #47028 · protein
Crystallographic analysis of a chemically modified triosephosphate isomerase from trypanosoma cruzi with dithiobenzylamine (dtba)
2OMA: “Crystallographic analysis of a chemically modified triosephosphate isomerase from trypanosoma cruzi with…”. X-ray diffraction, 1 ligand (SO4), 4 pockets (best druggability 0.44). MolNFT v1 #47028 on GenesisL1: 3D structure, binding…
- PDB
- 2OMA
- Type
- protein
- Length
- 500 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Triosephosphate isomerase
- EC
- 5.3.1.1
- UniProt
- P52270
- Ligands
- SO4
- Pockets
- 4 · best druggability 0.44
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Triosephosphate isomerase (EC 5.3.1.1) | protein | 250 | 48% helix, 17% strand | P52270 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 9 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, B
- PGE · Triethylene glycol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 125 | 0.44 | 0.77 | 27 | SO4 |
| 2 | 84 | 0.43 | 0.79 | 18 | empty |
| 3 | 90 | 0.38 | 0.76 | 16 | empty |
| 4 | 59 | 0.31 | 0.76 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1508 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- 2OMA · Crystallographic analysis of a chemically modified triosephosphate isomerase from… · the same entry in another collection · chain A against A, TM-score 1.00
- P52270 · AlphaFold monomer V2.0 prediction for triosephosphate isomerase, glycosomal (P52270) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P52270
- Elsewhere: RCSB PDB 2OMA · PDBe 2OMA · UniProt P52270
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.