Research workbench
Cholera toxin B-pentamer with decavalent ligand bmsc-0013
Analyse Cholera toxin B-pentamer with decavalent ligand bmsc-0013 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1MD2
- Type
- protein
- Length
- 515 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cholera toxin B subunit
- Ligands
- 233, SQ, CYN
- Pockets
- 4 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 25% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, E, F, G, H | Cholera toxin B subunit | protein | 103 | 25% helix, 36% strand | — |
Ligands and binding sites
- 233 · [5-(3,4,5-trihydroxy-6-hydroxymethyl-tetrahydro-pyran-2-ylcarbamoyl)-pentyl]-carbamic acid methyl ester · ligand · 5 copies · chains D, E, F
- SQ · 3-ethylamino-4-methylamino-cyclobutane-1,2-dione · ligand · 2 copies
- CYN · Cyanide ion · ion
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 | 1002 | 0.74 | 0.77 | 41 | empty |
| 2 | 61 | 0.42 | 0.82 | 18 | empty |
| 3 | 54 | 0.40 | 0.82 | 19 | empty |
| 4 | 52 | 0.28 | 0.75 | 10 | empty |
Interfaces
5 interfaces between chains.
- D–E · 1337 Ų buried · 25 hydrogen bonds · protein-protein
- G–H · 1323 Ų buried · 24 hydrogen bonds · protein-protein
- D–H · 1304 Ų buried · 23 hydrogen bonds · protein-protein
- F–G · 1299 Ų buried · 24 hydrogen bonds · protein-protein
- E–F · 1283 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 5 modified (disulfide, oxidation).
Compared structures
- 1MD2 · Cholera toxin B-pentamer with decavalent ligand bmsc-0013 · the same entry in another collection · chain D against D, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 1MD2 · PDBe 1MD2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.