Research workbench
Structural basis of human triosephosphate isomerase deficiency. mutation E104D and correlation to solvent perturbation.
Analyse Structural basis of human triosephosphate isomerase deficiency. mutation E104D… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VOM
- Type
- protein
- Length
- 978 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Triosephosphate isomerase
- EC
- 5.3.1.1
- UniProt
- P60174
- Pockets
- 6 · best druggability 0.66
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Triosephosphate isomerase (EC 5.3.1.1) | protein | 245 | 45% helix, 17% strand | P60174 |
| B | Triosephosphate isomerase (EC 5.3.1.1) | protein | 246 | 44% helix, 16% strand | P60174 |
| C | Triosephosphate isomerase (EC 5.3.1.1) | protein | 245 | 44% helix, 16% strand | P60174 |
| D | Triosephosphate isomerase (EC 5.3.1.1) | protein | 242 | 44% helix, 17% strand | P60174 |
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 615 | 0.66 | 0.76 | 60 | empty |
| 2 | 120 | 0.43 | 0.77 | 28 | empty |
| 3 | 98 | 0.41 | 0.77 | 29 | empty |
| 4 | 102 | 0.40 | 0.76 | 31 | empty |
| 5 | 110 | 0.39 | 0.75 | 29 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1770 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 1767 Ų buried · 34 hydrogen bonds · protein-protein
- A–C · 243 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 48 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2VOM · Structural basis of human triosephosphate isomerase deficiency. Mutation E104D and… · the same entry in another collection · chain D against D, TM-score 1.00
- P60174 · AlphaFold monomer V2.0 prediction for triosephosphate isomerase (P60174) · a predicted model of the same protein · chain B 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 P60174
- Elsewhere: RCSB PDB 2VOM · PDBe 2VOM · UniProt P60174
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