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Crystal structure of dimeric S33C beta-2 microglobulin mutant in complex with thioflavin (tht) at 2.8 ångström resolution
Analyse Crystal structure of dimeric S33C beta-2 microglobulin mutant in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RA3
- Type
- protein
- Length
- 395 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-2-microglobulin
- UniProt
- P61769
- Ligands
- TFX
- Pockets
- 4 · best druggability 0.57
Structure
x-ray diffraction · 3 distinct chains · 0% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-2-microglobulin | protein | 100 | 0% helix, 50% strand | P61769 |
| B | Beta-2-microglobulin | protein | 97 | 0% helix, 52% strand | P61769 |
| C, D | Beta-2-microglobulin | protein | 99 | 0% helix, 51% strand | P61769 |
Ligands and binding sites
- TFX · 2-[4-(dimethylamino)phenyl]-3,6-dimethyl-1,3-benzothiazol-3-ium · ligand · 5 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 402 | 0.57 | 0.75 | 29 | TFX |
| 2 | 324 | 0.56 | 0.76 | 25 | TFX |
| 3 | 94 | 0.42 | 0.78 | 19 | empty |
| 4 | 70 | 0.34 | 0.76 | 14 | empty |
Interfaces
5 interfaces between chains.
- A–C · 617 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 615 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 376 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 311 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 150 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 4RA3 · Crystal structure of dimeric S33C beta-2 microglobulin mutant in complex with Thioflavin… · the same entry in another collection · chain B against B, TM-score 1.00
- P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 P61769
- Elsewhere: RCSB PDB 4RA3 · PDBe 4RA3 · UniProt P61769
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