Research workbench
Crystal structure of the tetrameric beta-2 microglobulin DIMC20 mutant
Analyse Crystal structure of the tetrameric beta-2 microglobulin DIMC20 mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3TLR
- Type
- protein
- Length
- 400 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-2-microglobulin
- UniProt
- P61769
- Ligands
- CD, NA
- Pockets
- 7 · best druggability 0.60
Structure
x-ray diffraction · 1 distinct chain · 0% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
Ligands and binding sites
- CD · Cadmium ion · metal · 10 copies · chains A, C, D, B
- NA · Sodium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 345 | 0.60 | 0.77 | 50 | CD |
| 2 | 101 | 0.39 | 0.76 | 20 | empty |
| 3 | 103 | 0.38 | 0.75 | 19 | empty |
| 4 | 87 | 0.37 | 0.76 | 14 | empty |
| 5 | 110 | 0.36 | 0.74 | 16 | CD |
Interfaces
4 interfaces between chains.
- B–D · 651 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 649 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 471 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 471 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 3TLR · Crystal Structure of the tetrameric Beta-2 microglobulin DIMC20 mutant · the same entry in another collection · chain D against D, TM-score 1.00
- P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · 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 P61769
- Elsewhere: RCSB PDB 3TLR · PDBe 3TLR · UniProt P61769
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.