Research workbench
TAPASIN/ERP57 heterodimer
Analyse TAPASIN/ERP57 heterodimer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3F8U
- Type
- protein
- Length
- 1,653 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein disulfide-isomerase A3ERP57; Tapasin
- EC
- 5.3.4.1
- UniProt
- P30101, O15533
- Ligands
- NAG
- Pockets
- 15 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 21% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein disulfide-isomerase A3ERP57 (EC 5.3.4.1) | protein | 469 | 33% helix, 21% strand | P30101 |
| B | Tapasin | protein | 361 | 6% helix, 46% strand | O15533 |
| C | Protein disulfide-isomerase A3ERP57 (EC 5.3.4.1) | protein | 462 | 33% helix, 22% strand | P30101 |
| D | Tapasin | protein | 361 | 6% helix, 46% strand | O15533 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 793 | 0.72 | 0.78 | 78 | empty |
| 2 | 569 | 0.68 | 0.78 | 61 | empty |
| 3 | 489 | 0.67 | 0.78 | 59 | empty |
| 4 | 261 | 0.55 | 0.77 | 47 | empty |
| 5 | 265 | 0.54 | 0.76 | 31 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1141 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1086 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 631 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 94 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 3F8U · Tapasin/ERp57 heterodimer · the same entry in another collection · chain D against D, TM-score 1.00
- O15533 · AlphaFold monomer V2.0 prediction for tapasin (O15533) · a predicted model of the same protein · chain B against A, TM-score 0.99
- P30101 · AlphaFold monomer V2.0 prediction for protein disulfide-isomerase A3 (P30101) · 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 P30101
- Every structure of UniProt O15533
- Elsewhere: RCSB PDB 3F8U · PDBe 3F8U · UniProt P30101 · UniProt O15533
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