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
- 6ZT9
- Type
- protein
- Length
- 1,476 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
- 8 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 29% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-L-arabinofuranosidase (EC 3.2.1.55) | protein | 493 | 29% helix, 30% strand | O69262 |
| B | Alpha-L-arabinofuranosidase (EC 3.2.1.55) | protein | 491 | 29% helix, 30% strand | O69262 |
| C | Alpha-L-arabinofuranosidase (EC 3.2.1.55) | protein | 492 | 29% 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 · 21 copies · chains A, C, B
- ACT · Acetate ion · additive · 16 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
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1168 | 0.80 | 0.81 | 107 | AHR, ACT |
| 2 | 637 | 0.72 | 0.79 | 62 | AHR, ACT |
| 3 | 582 | 0.71 | 0.79 | 53 | AHR, ACT |
| 4 | 52 | 0.31 | 0.77 | 14 | empty |
| 5 | 57 | 0.29 | 0.75 | 12 | empty |
Interfaces
3 interfaces between chains.
- A–B · 928 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 927 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 921 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 1 covalent (disulfide, additive adduct).
Compared structures
- 6ZT9 · 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 6ZT9 · PDBe 6ZT9 · UniProt O69262
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