Research workbench
Crystal structure of the third catalytic domain of ERP46
Analyse Crystal structure of the third catalytic domain of ERP46 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3UVT
- Type
- protein
- Length
- 526 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thioredoxin domain-containing protein 5
- EC
- 5.3.4.1
- UniProt
- Q8NBS9
- Ligands
- SO4
- Pockets
- 5 · best druggability 0.51
Structure
x-ray diffraction · 5 distinct chains · 32% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thioredoxin domain-containing protein 5 (EC 5.3.4.1) | protein | 106 | 35% helix, 26% strand | Q8NBS9 |
| B | Thioredoxin domain-containing protein 5 (EC 5.3.4.1) | protein | 107 | 33% helix, 25% strand | Q8NBS9 |
| C | Thioredoxin domain-containing protein 5 (EC 5.3.4.1) | protein | 110 | 31% helix, 25% strand | Q8NBS9 |
| D | Thioredoxin domain-containing protein 5 (EC 5.3.4.1) | protein | 107 | 36% helix, 26% strand | Q8NBS9 |
| E | Thioredoxin domain-containing protein 5 (EC 5.3.4.1) | protein | 96 | 25% helix, 24% strand | Q8NBS9 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 181 | 0.51 | 0.77 | 30 | empty |
| 2 | 212 | 0.48 | 0.75 | 30 | empty |
| 3 | 77 | 0.43 | 0.81 | 20 | empty |
| 4 | 150 | 0.42 | 0.74 | 24 | empty |
| 5 | 54 | 0.28 | 0.75 | 14 | empty |
Interfaces
5 interfaces between chains.
- A–D · 558 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 287 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 221 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 116 Ų buried · 3 hydrogen bonds · protein-protein
- A–E · 38 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 3UVT · Crystal structure of the third catalytic domain of ERp46 · the same entry in another collection · chain E against E, TM-score 1.00
- Q8NBS9 · AlphaFold monomer V2.0 prediction for thioredoxin domain-containing protein 5 (Q8NBS9) · a predicted model of the same protein · chain A 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 Q8NBS9
- Elsewhere: RCSB PDB 3UVT · PDBe 3UVT · UniProt Q8NBS9
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