Research workbench
Crystal structure of triosephosphate isomerase sad deletion and N115A mutant from opisthorchis viverrini
Analyse Crystal structure of triosephosphate isomerase sad deletion and N115A mutant… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ZGA
- Type
- protein
- Length
- 972 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Triosephosphate isomerase
- EC
- 5.3.1.1
- UniProt
- A0A074Z863
- Pockets
- 9 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Triosephosphate isomerase (EC 5.3.1.1) | protein | 241 | 43% helix, 17% strand | A0A074Z863 |
| B, D | Triosephosphate isomerase (EC 5.3.1.1) | protein | 245 | 44% helix, 16% strand | A0A074Z863 |
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 953 | 0.81 | 0.82 | 126 | empty |
| 2 | 269 | 0.77 | 0.90 | 43 | empty |
| 3 | 98 | 0.76 | 0.97 | 28 | empty |
| 4 | 87 | 0.75 | 0.98 | 26 | empty |
| 5 | 69 | 0.44 | 0.81 | 23 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1679 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 1645 Ų buried · 28 hydrogen bonds · protein-protein
- A–D · 617 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 601 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 360 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5ZGA · Crystal Structure of Triosephosphate isomerase SAD deletion and N115A mutant from… · the same entry in another collection · chain A against A, TM-score 1.00
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 A0A074Z863
- Elsewhere: RCSB PDB 5ZGA · PDBe 5ZGA · UniProt A0A074Z863
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