Research workbench
Bacteroides ovatus xyloglucan pul GH43A in complex with aradnj
Analyse Bacteroides ovatus xyloglucan pul GH43A in complex with aradnj in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JOX
- Type
- protein
- Length
- 1,004 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Non-reducing end alpha-L-arabinofuranosidase BOGH43A
- EC
- 3.2.1.55
- UniProt
- A7LXT8
- Ligands
- EDG
- Pockets
- 12 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 4% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Non-reducing end alpha-L-arabinofuranosidase BOGH43A (EC 3.2.1.55) | protein | 502 | 4% helix, 50% strand | A7LXT8 |
| B | Non-reducing end alpha-L-arabinofuranosidase BOGH43A (EC 3.2.1.55) | protein | 502 | 4% helix, 48% strand | A7LXT8 |
Ligands and binding sites
- EDG · 1,4-dideoxy-1,4-imino-L-arabinitol · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 865 | 0.79 | 0.81 | 94 | EDG |
| 2 | 369 | 0.60 | 0.76 | 40 | empty |
| 3 | 303 | 0.58 | 0.77 | 36 | empty |
| 4 | 231 | 0.55 | 0.77 | 20 | empty |
| 5 | 218 | 0.54 | 0.78 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1347 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 5JOX · Bacteroides ovatus Xyloglucan PUL GH43A in complex with AraDNJ · the same entry in another collection · chain A against A, TM-score 1.00
- A7LXT8 · AlphaFold monomer V2.0 prediction for non-reducing end alpha-L- arabinofuranosidase… · 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 A7LXT8
- Elsewhere: RCSB PDB 5JOX · PDBe 5JOX · UniProt A7LXT8
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