Research workbench
Crystal structure of R67A mutant of alpha-L-arabinofuranosidase ARA51 from clostridium thermocellum
Analyse Crystal structure of R67A mutant of alpha-L-arabinofuranosidase ARA51 from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5O7Z
- Type
- protein
- Length
- 2,982 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Intracellular exo-alpha-(1->5)-L-arabinofuranosidase
- EC
- 3.2.1.55
- UniProt
- A3DIH0
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Intracellular exo-alpha-(1->5)-L-arabinofuranosidase (EC 3.2.1.55) | protein | 498 | 28% helix, 26% strand | A3DIH0 |
| B, E, F | Intracellular exo-alpha-(1->5)-L-arabinofuranosidase (EC 3.2.1.55) | protein | 496 | 30% helix, 26% strand | A3DIH0 |
Ligands and binding sites
- DIO · 1,4-diethylene dioxide · additive · 4 copies · chains C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1116 | 0.78 | 0.80 | 61 | empty |
| 2 | 1082 | 0.77 | 0.79 | 49 | empty |
| 3 | 990 | 0.69 | 0.74 | 77 | empty |
| 4 | 1185 | 0.69 | 0.74 | 116 | DIO |
| 5 | 468 | 0.57 | 0.74 | 55 | empty |
Interfaces
9 interfaces between chains.
- B–D · 893 Ų buried · 9 hydrogen bonds · protein-protein
- C–E · 853 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 777 Ų buried · 11 hydrogen bonds · protein-protein
- D–F · 773 Ų buried · 8 hydrogen bonds · protein-protein
- C–F · 768 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 5O7Z · Crystal Structure of R67A Mutant of alpha-L-arabinofuranosidase Ara51 from Clostridium… · the same entry in another collection · chain F against F, TM-score 1.00
- A3DIH0 · AlphaFold monomer V2.0 prediction for intracellular exo… · a predicted model of the same protein · chain B 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 A3DIH0
- Elsewhere: RCSB PDB 5O7Z · PDBe 5O7Z · UniProt A3DIH0
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