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Crystal structure of ERP46 TRX1
Analyse Crystal structure of ERP46 TRX1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WGD
- Type
- protein
- Length
- 995 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thioredoxin domain-containing protein 5
- UniProt
- Q8NBS9
- Ligands
- K, PO4
- Pockets
- 6 · best druggability 0.68
Structure
x-ray diffraction · 5 distinct chains · 41% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, E, I | Thioredoxin domain-containing protein 5 | protein | 111 | 41% helix, 21% strand | Q8NBS9 |
| C | Thioredoxin domain-containing protein 5 | protein | 112 | 40% helix, 18% strand | Q8NBS9 |
| F | Thioredoxin domain-containing protein 5 | protein | 109 | 41% helix, 18% strand | Q8NBS9 |
| G | Thioredoxin domain-containing protein 5 | protein | 109 | 41% helix, 21% strand | Q8NBS9 |
| H | Thioredoxin domain-containing protein 5 | protein | 110 | 41% helix, 20% strand | Q8NBS9 |
Ligands and binding sites
- K · Potassium ion · metal · 5 copies · chains C, B, E, A, F, I
- PO4 · Phosphate ion · ion · 15 copies · chains A, F, B, C, D, E, G, H, I
- GOL · Glycerol · additive · 11 copies · chains A, B, F, C, E, G, H, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 444 | 0.68 | 0.80 | 54 | empty |
| 2 | 211 | 0.60 | 0.81 | 29 | empty |
| 3 | 148 | 0.49 | 0.78 | 28 | empty |
| 4 | 67 | 0.30 | 0.74 | 23 | empty |
| 5 | 54 | 0.29 | 0.75 | 11 | PO4 |
Interfaces
9 interfaces between chains.
- A–F · 522 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 521 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 515 Ų buried · 10 hydrogen bonds · protein-protein
- B–E · 499 Ų buried · 6 hydrogen bonds · protein-protein
- G–H · 494 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 disulfide (disulfide).
Compared structures
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 Q8NBS9
- Elsewhere: RCSB PDB 3WGD · PDBe 3WGD · UniProt Q8NBS9
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