Research workbench
Crystal structure of alpha-L-arabinofuranosidase from thermotoga maritima xylose complex
Analyse Crystal structure of alpha-L-arabinofuranosidase from thermotoga maritima… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3UG5
- Type
- protein
- Length
- 2,892 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-L-arabinofuranosidase
- EC
- 3.2.1.55
- UniProt
- Q9WYB7
- Ligands
- XYP
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 29% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E, F | Alpha-L-arabinofuranosidase (EC 3.2.1.55) | protein | 482 | 29% helix, 32% strand | Q9WYB7 |
| C | Alpha-L-arabinofuranosidase (EC 3.2.1.55) | protein | 483 | 29% helix, 31% strand | Q9WYB7 |
| D | Alpha-L-arabinofuranosidase (EC 3.2.1.55) | protein | 481 | 29% helix, 31% strand | Q9WYB7 |
Ligands and binding sites
- XYP · beta-D-xylopyranose · sugar · 15 copies · chains A, D, B, E, C, F
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 12 copies · chains A, B, C, D, F, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1022 | 0.74 | 0.77 | 55 | empty |
| 2 | 1090 | 0.73 | 0.77 | 62 | empty |
| 3 | 1195 | 0.72 | 0.76 | 119 | XYP |
| 4 | 585 | 0.71 | 0.79 | 70 | TRS, XYP |
| 5 | 86 | 0.69 | 0.93 | 18 | TRS |
Interfaces
9 interfaces between chains.
- D–F · 715 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 708 Ų buried · 9 hydrogen bonds · protein-protein
- D–E · 708 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 705 Ų buried · 8 hydrogen bonds · protein-protein
- E–F · 703 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 3UG5 · Crystal structure of alpha-L-arabinofuranosidase from Thermotoga maritima xylose complex · 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 Q9WYB7
- Elsewhere: RCSB PDB 3UG5 · PDBe 3UG5 · UniProt Q9WYB7
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