Research workbench
Crystal structure of the beta-2 microglobulin DIMC50 disulphide-linked homodimer mutant
Analyse Crystal structure of the beta-2 microglobulin DIMC50 disulphide-linked… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3TM6
- Type
- protein
- Length
- 787 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-2-microglobulin
- UniProt
- P61769
- Ligands
- PO4
- Pockets
- 9 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 0% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Beta-2-microglobulin | protein | 99 | 0% helix, 51% strand | P61769 |
| C, E, F, G, H | Beta-2-microglobulin | protein | 98 | 0% helix, 51% strand | P61769 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 6 copies · chains B, D, A, C, E, H, F, G
- PEG · Di(hydroxyethyl)ether · additive · 5 copies · chains A, B, C, D, E, F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 646 | 0.76 | 0.82 | 64 | PO4, PEG |
| 2 | 551 | 0.72 | 0.80 | 68 | PEG, PO4 |
| 3 | 377 | 0.72 | 0.83 | 54 | PEG |
| 4 | 549 | 0.64 | 0.76 | 41 | empty |
| 5 | 186 | 0.63 | 0.84 | 26 | PEG |
Interfaces
15 interfaces between chains.
- B–C · 630 Ų buried · 6 hydrogen bonds · protein-protein
- E–G · 627 Ų buried · 4 hydrogen bonds · protein-protein
- F–H · 621 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 599 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 366 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 3TM6 · Crystal structure of the beta-2 microglobulin DIMC50 disulphide-linked homodimer mutant · the same entry in another collection · chain H against H, TM-score 1.00
- P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain E 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 3TM6 · PDBe 3TM6 · UniProt P61769
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.