MolNFT v1 · #51676 · protein
Structure-based enzyme engineering efforts with an inactive monomeric tim variant: the importance of a single point mutation for generating an active site with suitable binding properties
2VEM · Glycosomal triosephosphate isomerase: “Structure-based enzyme engineering efforts with an inactive monomeric tim variant: the importance of a single…”. X-ray diffraction, 1 ligand (BBR), 3 pockets (best druggability 0.80). MolNFT v1…
- PDB
- 2VEM
- Type
- protein
- Length
- 472 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycosomal triosephosphate isomerase
- EC
- 5.3.1.1
- UniProt
- P04789
- Ligands
- BBR
- Pockets
- 3 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycosomal triosephosphate isomerase (EC 5.3.1.1) | protein | 234 | 46% helix, 17% strand | P04789 |
| B | Glycosomal triosephosphate isomerase (EC 5.3.1.1) | protein | 238 | 47% helix, 17% strand | P04789 |
Ligands and binding sites
- BBR · (3-bromo-2-oxo-propoxy)phosphonic acid · ligand · 2 copies · chains A, B
- TBU · Tertiary-butyl alcohol · additive · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1172 | 0.80 | 0.81 | 104 | empty |
| 2 | 81 | 0.42 | 0.80 | 23 | BBR |
| 3 | 79 | 0.40 | 0.78 | 19 | BBR |
Interfaces
1 interface between chains.
- A–B · 649 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 2VEM · Structure-based enzyme engineering efforts with an inactive monomeric TIM variant: the… · the same entry in another collection · chain A 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 0.99
- 4TIM · Crystallographic and molecular modeling studies on trypanosomal triosephosphate… · a predicted model of the same protein · chain A against A, TM-score 0.97
- 4TIM · Crystallographic and molecular modeling studies on trypanosomal triosephosphate… · a predicted model of the same protein · chain A against A, TM-score 0.97
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 2VEM · PDBe 2VEM · UniProt P04789
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