Research workbench
Heat-labile enterotoxin B-pentamer with ligand bmsc-0010
Analyse Heat-labile enterotoxin B-pentamer with ligand bmsc-0010 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1JQY
- Type
- protein
- Length
- 1,545 residues
- Chains
- 15
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heat-labile enterotoxin B chain
- UniProt
- P32890
- Ligands
- A32
- Pockets
- 17 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 22% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, E, F, G, H, L, M, N, O, P, V, W, X, Y, Z | Heat-labile enterotoxin B chain | protein | 103 | 22% helix, 41% strand | P32890 |
Ligands and binding sites
- A32 · (3-nitro-5-(3-morpholin-4-yl-propylaminocarbonyl)phenyl)-galactopyranoside · ligand · 14 copies · chains D, E, F, G, H, L, M, N, O, P, V, W, X, Y, Z
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1106 | 0.75 | 0.78 | 43 | empty |
| 2 | 1077 | 0.75 | 0.77 | 45 | empty |
| 3 | 1040 | 0.74 | 0.77 | 46 | empty |
| 4 | 59 | 0.41 | 0.81 | 16 | empty |
| 5 | 62 | 0.39 | 0.80 | 22 | empty |
Interfaces
17 interfaces between chains.
- N–O · 1407 Ų buried · 29 hydrogen bonds · protein-protein
- F–G · 1397 Ų buried · 32 hydrogen bonds · protein-protein
- D–E · 1393 Ų buried · 30 hydrogen bonds · protein-protein
- W–X · 1387 Ų buried · 34 hydrogen bonds · protein-protein
- D–H · 1386 Ų buried · 29 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 disulfide (disulfide).
Compared structures
- 1JQY · Heat-labile enterotoxin B-pentamer with ligand bmsc-0010 · the same entry in another collection · chain V against V, 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
- Every structure of UniProt P32890
- Elsewhere: RCSB PDB 1JQY · PDBe 1JQY · UniProt P32890
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