Research workbench
Crystal structure of the B'-a' domain of thermophilic fungal protein disulfide isomerase (reduced form)
Analyse Crystal structure of the B'-a' domain of thermophilic fungal protein disulfide… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WT1
- Type
- protein
- Length
- 970 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein disulfide-isomerase
- EC
- 5.3.4.1
- UniProt
- P55059
- Pockets
- 11 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein disulfide-isomerase (EC 5.3.4.1) | protein | 244 | 34% helix, 20% strand | P55059 |
| B, C, D | Protein disulfide-isomerase (EC 5.3.4.1) | protein | 242 | 35% helix, 20% strand | P55059 |
Ligands and binding sites
- GOL · Glycerol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 539 | 0.60 | 0.74 | 40 | empty |
| 2 | 452 | 0.60 | 0.75 | 40 | empty |
| 3 | 291 | 0.58 | 0.77 | 25 | empty |
| 4 | 194 | 0.48 | 0.75 | 26 | empty |
| 5 | 164 | 0.44 | 0.75 | 25 | empty |
Interfaces
6 interfaces between chains.
- B–C · 416 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 260 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 133 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 123 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 85 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3WT1 · Crystal structure of the b'-a' domain of thermophilic fungal protein disulfide isomerase… · the same entry in another collection · chain B against B, TM-score 1.00
- P55059 · AlphaFold monomer V2.0 prediction for protein disulfide-isomerase (P55059) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 P55059
- Elsewhere: RCSB PDB 3WT1 · PDBe 3WT1 · UniProt P55059
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.