MolNFT v1 · #52022 · protein
Structural basis of human triosephosphate isomerase deficiency. mutation E104D and correlation to solvent perturbation.
2VOM: “Structural basis of human triosephosphate isomerase deficiency. mutation E104D and correlation to solvent…”. X-ray diffraction, 6 pockets (best druggability 0.66). MolNFT v1 #52022 on GenesisL1: 3D structure, binding sites and…
- 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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