Research workbench
Elucidation of the substrate specificity and protein structure of abfb, a family 51 alpha-L-arabinofuranosidase from bifidobacterium longum.
Analyse Elucidation of the substrate specificity and protein structure of abfb, a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Y2W
- Type
- protein
- Length
- 3,062 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Arabinofuranosidase
- EC
- 3.2.1.55
- UniProt
- Q841V6
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 6 distinct chains · 29% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Arabinofuranosidase (EC 3.2.1.55) | protein | 505 | 29% helix, 26% strand | Q841V6 |
| B | Arabinofuranosidase (EC 3.2.1.55) | protein | 505 | 27% helix, 25% strand | Q841V6 |
| C | Arabinofuranosidase (EC 3.2.1.55) | protein | 504 | 29% helix, 26% strand | Q841V6 |
| D | Arabinofuranosidase (EC 3.2.1.55) | protein | 511 | 30% helix, 25% strand | Q841V6 |
| E | Arabinofuranosidase (EC 3.2.1.55) | protein | 519 | 30% helix, 25% strand | Q841V6 |
| F | Arabinofuranosidase (EC 3.2.1.55) | protein | 518 | 31% helix, 26% strand | Q841V6 |
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1096 | 0.79 | 0.80 | 55 | empty |
| 2 | 1200 | 0.78 | 0.80 | 51 | empty |
| 3 | 67 | 0.72 | 0.97 | 19 | empty |
| 4 | 76 | 0.72 | 0.96 | 18 | empty |
| 5 | 616 | 0.71 | 0.79 | 88 | empty |
Interfaces
9 interfaces between chains.
- B–E · 1299 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1285 Ų buried · 11 hydrogen bonds · protein-protein
- E–F · 1280 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 1144 Ų buried · 15 hydrogen bonds · protein-protein
- B–F · 1110 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 2Y2W · Elucidation of the substrate specificity and protein structure of AbfB, a family 51… · the same entry in another collection · chain F against F, TM-score 1.00
- Q841V6 · AlphaFold monomer V2.0 prediction for intracellular exo… · a predicted model of the same protein · chain C against A, TM-score 0.99
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 Q841V6
- Elsewhere: RCSB PDB 2Y2W · PDBe 2Y2W · UniProt Q841V6
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