MolNFT v1 · #72150 · protein
Protein-induced photophysical changes to the amyloid indicator dye, thioflavin T
3MZT · Beta-2-microglobulin: “Protein-induced photophysical changes to the amyloid indicator dye, thioflavin T”. X-ray diffraction, 2 ligands (TFX, CU), 13 pockets (best druggability 0.64). MolNFT v1 #72150 on GenesisL1: 3D structure…
- PDB
- 3MZT
- Type
- protein
- Length
- 600 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-2-microglobulin
- UniProt
- P61769
- Ligands
- TFX, CU
- Pockets
- 13 · best druggability 0.64
Structure
x-ray diffraction · 1 distinct chain · 0% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
Ligands and binding sites
- TFX · 2-[4-(dimethylamino)phenyl]-3,6-dimethyl-1,3-benzothiazol-3-ium · ligand · 3 copies · chains B, C, D, E, A, F
- CU · Copper (II) ion · metal · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 434 | 0.64 | 0.77 | 50 | TFX |
| 2 | 451 | 0.63 | 0.77 | 55 | TFX |
| 3 | 397 | 0.60 | 0.76 | 42 | TFX |
| 4 | 146 | 0.45 | 0.76 | 29 | empty |
| 5 | 62 | 0.43 | 0.82 | 23 | empty |
Interfaces
6 interfaces between chains.
- A–F · 1065 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 1028 Ų buried · 10 hydrogen bonds · protein-protein
- D–E · 975 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 719 Ų buried · 13 hydrogen bonds · protein-protein
- E–F · 717 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 3MZT · Protein-induced photophysical changes to the amyloid indicator dye, thioflavin T · the same entry in another collection · chain F against F, TM-score 1.00
- P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain D against A, TM-score 0.92
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 3MZT · PDBe 3MZT · UniProt P61769
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