MolNFT v1 · #172152 · protein
X-ray structure of mutated arabinofuranosidase
6ZT8 · Alpha-L-arabinofuranosidase: “X-ray structure of mutated arabinofuranosidase”. X-ray diffraction, 1 ligand (CL), 10 pockets (best druggability 0.81). MolNFT v1 #172152 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6ZT8
- Type
- protein
- Length
- 1,470 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
- CL
- Pockets
- 10 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Alpha-L-arabinofuranosidase (EC 3.2.1.55) | protein | 490 | 29% helix, 30% strand | O69262 |
Ligands and binding sites
- CL · Chloride ion · ion · 3 copies · chains A, B, C
- PG4 · Tetraethylene glycol · additive · 4 copies · chains A, B, C
- 1PE · Pentaethylene glycol · additive · 2 copies · chains A, B
- PGE · Triethylene glycol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1038 | 0.81 | 0.82 | 92 | empty |
| 2 | 654 | 0.73 | 0.79 | 48 | empty |
| 3 | 449 | 0.72 | 0.82 | 43 | empty |
| 4 | 86 | 0.43 | 0.79 | 17 | empty |
| 5 | 85 | 0.41 | 0.78 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–B · 919 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 899 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 883 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 6ZT8 · 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 6ZT8 · PDBe 6ZT8 · UniProt O69262
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