Research workbench
X-ray structure of mutated arabinofuranosidase
Analyse X-ray structure of mutated arabinofuranosidase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZT7
- Type
- protein
- Length
- 1,473 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-L-arabinofuranosidase
- EC
- 3.2.1.55
- UniProt
- O69262
- Ligands
- AHR
- Pockets
- 9 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Alpha-L-arabinofuranosidase (EC 3.2.1.55) | protein | 491 | 30% helix, 30% strand | O69262 |
Ligands and binding sites
- AHR · alpha-L-arabinofuranose · sugar · 3 copies · chains A, B, C
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 28 copies · chains A, B, C
- ACT · Acetate ion · additive · 17 copies · chains A, B, C
- BTB · 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 534 | 0.75 | 0.83 | 51 | empty |
| 2 | 615 | 0.73 | 0.80 | 55 | AHR |
| 3 | 626 | 0.72 | 0.79 | 55 | AHR |
| 4 | 625 | 0.71 | 0.78 | 63 | AHR |
| 5 | 59 | 0.34 | 0.77 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–B · 933 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 912 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 911 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 6ZT7 · X-ray structure of mutated arabinofuranosidase · 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 O69262
- Elsewhere: RCSB PDB 6ZT7 · PDBe 6ZT7 · UniProt O69262
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.