MolNFT v1 · #141683 · protein
Crystal structure of triosephosphate isomerase from opisthorchis viverrini
5ZFX: “Crystal structure of triosephosphate isomerase from opisthorchis viverrini”. X-ray diffraction, 1 ligand (MG), 11 pockets (best druggability 0.76). MolNFT v1 #141683 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5ZFX
- 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
- A0A074Z863
- Ligands
- MG
- Pockets
- 11 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Triosephosphate isomerase (EC 5.3.1.1) | protein | 244 | 46% helix, 17% strand | A0A074Z863 |
| B | Triosephosphate isomerase (EC 5.3.1.1) | protein | 248 | 47% helix, 16% strand | A0A074Z863 |
| C, D | Triosephosphate isomerase (EC 5.3.1.1) | protein | 243 | 46% helix, 17% strand | A0A074Z863 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 90 | 0.76 | 0.98 | 28 | empty |
| 2 | 88 | 0.76 | 0.98 | 28 | empty |
| 3 | 104 | 0.71 | 0.93 | 22 | empty |
| 4 | 246 | 0.66 | 0.83 | 28 | empty |
| 5 | 72 | 0.43 | 0.81 | 23 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1673 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 1671 Ų buried · 28 hydrogen bonds · protein-protein
- A–C · 449 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 42 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5ZFX · Crystal Structure of Triosephosphate isomerase from Opisthorchis viverrini · the same entry in another collection · chain D against D, 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 5ZFX · PDBe 5ZFX · UniProt A0A074Z863
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