MolNFT v1 · #129023 · protein
Crystal structure of R67A mutant of alpha-L-arabinofuranosidase ARA51 from clostridium thermocellum in complex with L-arabinofuranose
5O80 · Intracellular exo-alpha-(1->5)-L-arabinofuranosidase: “Crystal structure of R67A mutant of alpha-L-arabinofuranosidase ARA51 from clostridium thermocellum in…”. X-ray diffraction, 1 ligand (AHR), 20 pockets (best druggability 0.77).…
- PDB
- 5O80
- Type
- protein
- Length
- 2,976 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
- Ligands
- AHR
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Intracellular exo-alpha-(1->5)-L-arabinofuranosidase (EC 3.2.1.55) | protein | 496 | 29% helix, 25% strand | A3DIH0 |
Ligands and binding sites
- AHR · alpha-L-arabinofuranose · sugar · 6 copies · chains A, B, C, D, E, F
- DIO · 1,4-diethylene dioxide · additive · 6 copies · chains A, B, 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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1059 | 0.77 | 0.80 | 50 | empty |
| 2 | 1157 | 0.77 | 0.80 | 53 | empty |
| 3 | 922 | 0.69 | 0.74 | 84 | empty |
| 4 | 54 | 0.67 | 0.96 | 22 | empty |
| 5 | 648 | 0.63 | 0.74 | 76 | empty |
Interfaces
9 interfaces between chains.
- A–B · 871 Ų buried · 8 hydrogen bonds · protein-protein
- D–F · 869 Ų buried · 8 hydrogen bonds · protein-protein
- B–F · 772 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 764 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 763 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5O80 · Crystal Structure of R67A Mutant of alpha-L-arabinofuranosidase Ara51 from Clostridium… · the same entry in another collection · chain C against C, TM-score 1.00
- A3DIH0 · AlphaFold monomer V2.0 prediction for intracellular exo… · a predicted model of the same protein · 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 A3DIH0
- Elsewhere: RCSB PDB 5O80 · PDBe 5O80 · UniProt A3DIH0
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