Research workbench
Modular mutagenesis of a tim-barrel enzyme: the crystal structure of a chimeric E. COLI tim having the eighth (beta-alpha)-unit replaced by the equivalent unit of chicken tim
Analyse Modular mutagenesis of a tim-barrel enzyme: the crystal structure of a chimeric… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1TMH
- Type
- protein
- Length
- 1,016 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Triosephosphate isomerase
- EC
- 5.3.1.1
- UniProt
- P0A858
- Ligands
- SO4
- Pockets
- 9 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Triosephosphate isomerase (EC 5.3.1.1) | protein | 254 | 48% helix, 15% strand | P0A858 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 672 | 0.72 | 0.79 | 78 | SO4 |
| 2 | 315 | 0.69 | 0.83 | 48 | empty |
| 3 | 315 | 0.68 | 0.83 | 44 | empty |
| 4 | 83 | 0.49 | 0.83 | 20 | SO4 |
| 5 | 76 | 0.46 | 0.82 | 21 | SO4 |
Interfaces
4 interfaces between chains.
- A–B · 1719 Ų buried · 38 hydrogen bonds · protein-protein
- C–D · 1715 Ų buried · 39 hydrogen bonds · protein-protein
- A–D · 245 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 67 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1TMH · Modular mutagenesis of a tim-barrel enzyme: the crystal structure of a chimeric E. COLI… · the same entry in another collection · chain A against A, TM-score 1.00
- P0A858 · AlphaFold monomer V2.0 prediction for triosephosphate isomerase (P0A858) · 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 P0A858
- Elsewhere: RCSB PDB 1TMH · PDBe 1TMH · UniProt P0A858
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