Research workbench
Mcg immunoglobulin variable domain with methylene blue
Analyse Mcg immunoglobulin variable domain with methylene blue in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ACM
- Type
- protein
- Length
- 218 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mcg
- UniProt
- P01709
- Ligands
- MBT, SO4
- Pockets
- 4 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 3% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Mcg | protein | 109 | 3% helix, 49% strand | P01709 |
Ligands and binding sites
- MBT · 3,7-bis(dimethylamino)phenothiazin-5-ium · ligand · chains A, B
- SO4 · Sulfate ion · ion · 6 copies · chains A, B
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 421 | 0.70 | 0.80 | 32 | SO4 |
| 2 | 97 | 0.39 | 0.76 | 18 | empty |
| 3 | 61 | 0.34 | 0.76 | 10 | MBT |
| 4 | 63 | 0.32 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 521 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5ACM · Mcg immunoglobulin variable domain with methylene blue · the same entry in another collection · chain A against A, TM-score 1.00
- P01709 · AlphaFold monomer V2.0 prediction for immunoglobulin lambda variable 2-8 (P01709) · a predicted model of the same protein · chain A against A, TM-score 0.85
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 P01709
- Elsewhere: RCSB PDB 5ACM · PDBe 5ACM · UniProt P01709
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.