Research workbench
Intramolecular chaperone
Analyse Intramolecular chaperone in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GW6
- Type
- protein
- Length
- 1,531 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endo-N-acetylneuraminidase
- EC
- 3.2.1.129
- UniProt
- Q858B1
- Ligands
- TAM, CA, CL, BR
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 6 distinct chains · 22% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endo-N-acetylneuraminidase (EC 3.2.1.129) | protein | 256 | 21% helix, 41% strand | Q858B1 |
| B | Endo-N-acetylneuraminidase (EC 3.2.1.129) | protein | 255 | 22% helix, 41% strand | Q858B1 |
| E | Endo-N-acetylneuraminidase (EC 3.2.1.129) | protein | 257 | 23% helix, 40% strand | Q858B1 |
| C | Endo-N-acetylneuraminidase (EC 3.2.1.129) | protein | 254 | 20% helix, 41% strand | Q858B1 |
| D | Endo-N-acetylneuraminidase (EC 3.2.1.129) | protein | 252 | 22% helix, 40% strand | Q858B1 |
| F | Endo-N-acetylneuraminidase (EC 3.2.1.129) | protein | 257 | 23% helix, 40% strand | Q858B1 |
Ligands and binding sites
- TAM · Tris(hydroxyethyl)aminomethane · ligand · 3 copies · chains A, B, F, E, C
- CA · Calcium ion · metal · chains B, F
- CL · Chloride ion · ion · 6 copies · chains A, E, C, D
- BR · Bromide ion · ion · 6 copies · chains B, A, E, C, D, F
- PEG · Di(hydroxyethyl)ether · additive · 18 copies · chains A, F, B, E, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 58 | 0.74 | 0.99 | 12 | empty |
| 2 | 52 | 0.73 | 1.00 | 13 | empty |
| 3 | 142 | 0.66 | 0.88 | 32 | CA |
| 4 | 395 | 0.65 | 0.79 | 54 | TAM, BR |
| 5 | 165 | 0.65 | 0.85 | 35 | BR |
Interfaces
7 interfaces between chains.
- A–F · 6132 Ų buried · 122 hydrogen bonds · protein-protein
- E–C · 6128 Ų buried · 119 hydrogen bonds · protein-protein
- B–F · 6126 Ų buried · 124 hydrogen bonds · protein-protein
- A–B · 6061 Ų buried · 114 hydrogen bonds · protein-protein
- E–D · 6041 Ų buried · 113 hydrogen bonds · protein-protein
Compared structures
- 3GW6 · Intramolecular Chaperone · the same entry in another collection · chain E against E, 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 Q858B1
- Elsewhere: RCSB PDB 3GW6 · PDBe 3GW6 · UniProt Q858B1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.