Research workbench
The A178L mutation in the C-terminal hinge of the flexible loop-6 of triosephosphate isomerase (tim) induces a more closed conformation of this hinge region in dimeric and monomeric tim
Analyse The A178L mutation in the C-terminal hinge of the flexible loop-6 of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2V0T
- Type
- protein
- Length
- 1,960 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Triosephosphate isomerase glycosomal
- EC
- 5.3.1.1
- UniProt
- P04789
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Triosephosphate isomerase glycosomal (EC 5.3.1.1) | protein | 243 | 47% helix, 17% strand | P04789 |
| B, D, G | Triosephosphate isomerase glycosomal (EC 5.3.1.1) | protein | 249 | 46% helix, 17% strand | P04789 |
| C, F, H | Triosephosphate isomerase glycosomal (EC 5.3.1.1) | protein | 242 | 46% helix, 17% strand | P04789 |
| E | Triosephosphate isomerase glycosomal (EC 5.3.1.1) | protein | 244 | 44% helix, 18% strand | P04789 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 10 copies · chains A, B, C, D, E, F, G, H
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 652 | 0.78 | 0.84 | 56 | empty |
| 2 | 562 | 0.74 | 0.81 | 73 | empty |
| 3 | 361 | 0.56 | 0.75 | 44 | SO4 |
| 4 | 267 | 0.53 | 0.75 | 27 | empty |
| 5 | 148 | 0.47 | 0.77 | 40 | SO4 |
Interfaces
10 interfaces between chains.
- A–B · 1580 Ų buried · 30 hydrogen bonds · protein-protein
- C–E · 1572 Ų buried · 30 hydrogen bonds · protein-protein
- D–F · 1567 Ų buried · 36 hydrogen bonds · protein-protein
- G–H · 1565 Ų buried · 32 hydrogen bonds · protein-protein
- E–F · 278 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 2V0T · The A178L mutation in the C-terminal hinge of the flexible loop-6 of triosephosphate… · 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 1.00
- 4TIM · Crystallographic and molecular modeling studies on trypanosomal triosephosphate… · a predicted model of the same protein · chain D 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 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 P04789
- Elsewhere: RCSB PDB 2V0T · PDBe 2V0T · UniProt P04789
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