Research workbench
GM1 bound form of the ecx AB5 holotoxin
Analyse GM1 bound form of the ecx AB5 holotoxin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4L6T
- Type
- protein
- Length
- 774 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ecxa; Ecxb
- EC
- 3.4.24.-
- UniProt
- Q8GAV4, Q8GAV3
- Ligands
- GAL, BGC, NGA, SIA, ZN
- Pockets
- 8 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ecxa (EC 3.4.24.-) | protein | 249 | 37% helix, 21% strand | Q8GAV4 |
| B, C, D, E, F | Ecxb | protein | 105 | 24% helix, 36% strand | Q8GAV3 |
Ligands and binding sites
- GAL · beta-D-galactopyranose · sugar · 10 copies · chains B, C, D, E, F
- BGC · beta-D-glucopyranose · sugar · 5 copies
- NGA · 2-acetamido-2-deoxy-beta-D-galactopyranose · sugar · 5 copies · chains B, C, D, E, F
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 5 copies · chains B, C, D, E, F
- ZN · Zinc ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 985 | 0.83 | 0.84 | 68 | empty |
| 2 | 308 | 0.62 | 0.79 | 35 | empty |
| 3 | 443 | 0.61 | 0.76 | 59 | empty |
| 4 | 411 | 0.61 | 0.77 | 46 | empty |
| 5 | 51 | 0.32 | 0.77 | 14 | empty |
Interfaces
10 interfaces between chains.
- B–F · 1360 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 1351 Ų buried · 30 hydrogen bonds · protein-protein
- E–F · 1332 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 1327 Ų buried · 28 hydrogen bonds · protein-protein
- D–E · 1313 Ų buried · 31 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 4L6T · GM1 bound form of the ECX AB5 holotoxin · the same entry in another collection · chain A against A, 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 Q8GAV4
- Every structure of UniProt Q8GAV3
- Elsewhere: RCSB PDB 4L6T · PDBe 4L6T · UniProt Q8GAV4 · UniProt Q8GAV3
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