Research workbench
Thermotoga maritima family 1 glycoside hydrolase complexed with carba- cyclophellitol transition state mimic
Analyse Thermotoga maritima family 1 glycoside hydrolase complexed with carba… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5N6S
- Type
- protein
- Length
- 1,745 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-glucosidase a
- EC
- 3.2.1.21
- UniProt
- Q08638
- Ligands
- 8P5, CL
- Pockets
- 14 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-glucosidase a (EC 3.2.1.21) | protein | 443 | 46% helix, 19% strand | Q08638 |
| C | Beta-glucosidase a (EC 3.2.1.21) | protein | 428 | 45% helix, 18% strand | Q08638 |
| D | Beta-glucosidase a (EC 3.2.1.21) | protein | 431 | 44% helix, 17% strand | Q08638 |
Ligands and binding sites
- 8P5 · Azanylidene-[4-[[(1~{S},2~{R},3~{R},4~{R},5~{S},6~{S}, 7~{S})-2-(hydroxymethyl)-3,4,5-tris(oxidanyl)-7-bicyclo[4.1.0]heptanyl]carbonylamino]butylimino]azaniu M · ligand · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 6 copies · chains A, C, B, D
- EDO · 1,2-ethanediol · additive · 18 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains B, C
- IMD · Imidazole · additive · chains A
- PGE · Triethylene glycol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 564 | 0.75 | 0.82 | 55 | 8P5, ACT |
| 2 | 593 | 0.73 | 0.80 | 54 | 8P5 |
| 3 | 458 | 0.73 | 0.82 | 45 | EDO, 8P5 |
| 4 | 485 | 0.71 | 0.80 | 45 | EDO, 8P5 |
| 5 | 519 | 0.66 | 0.78 | 51 | CL, EDO |
Interfaces
5 interfaces between chains.
- A–C · 1115 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 378 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 75 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 45 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 17 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (additive adduct).
Compared structures
- 5N6S · Thermotoga maritima family 1 Glycoside hydrolase complexed with Carba-Cyclophellitol… · the same entry in another collection · chain D against D, TM-score 1.00
- Q08638 · AlphaFold monomer V2.0 prediction for beta-glucosidase a (Q08638) · a predicted model of the same protein · 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 Q08638
- Elsewhere: RCSB PDB 5N6S · PDBe 5N6S · UniProt Q08638
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.