MolNFT v1 · #33055 · protein
The structure of a family 51 arabinofuranosidase, ARAF51, from clostridium thermocellum in complex with 1,3-linked arabinoside of xylobiose.
2C8N · Alpha-L-arabinofuranosidase: “The structure of a family 51 arabinofuranosidase, ARAF51, from clostridium thermocellum in complex with…”. X-ray diffraction, 2 ligands (XYS, AHR), 20 pockets (best druggability 0.78). MolNFT v1 #33055…
- PDB
- 2C8N
- Type
- protein
- Length
- 2,992 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
- Q4CJG5
- Ligands
- XYS, AHR
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 6 distinct chains · 29% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-L-arabinofuranosidase (EC 3.2.1.55) | protein | 501 | 29% helix, 26% strand | Q4CJG5 |
| B | Alpha-L-arabinofuranosidase (EC 3.2.1.55) | protein | 499 | 28% helix, 24% strand | Q4CJG5 |
| C | Alpha-L-arabinofuranosidase (EC 3.2.1.55) | protein | 499 | 28% helix, 25% strand | Q4CJG5 |
| D | Alpha-L-arabinofuranosidase (EC 3.2.1.55) | protein | 496 | 29% helix, 25% strand | Q4CJG5 |
| E | Alpha-L-arabinofuranosidase (EC 3.2.1.55) | protein | 497 | 30% helix, 24% strand | Q4CJG5 |
| F | Alpha-L-arabinofuranosidase (EC 3.2.1.55) | protein | 500 | 27% helix, 26% strand | Q4CJG5 |
Ligands and binding sites
- XYS · alpha-D-xylopyranose · sugar · 6 copies · chains A, B, C, D, E, F
- AHR · alpha-L-arabinofuranose · sugar · 6 copies · chains A, B, C, D, E, F
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, D, F, B, C, 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, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1052 | 0.78 | 0.80 | 51 | empty |
| 2 | 1057 | 0.77 | 0.79 | 53 | empty |
| 3 | 967 | 0.69 | 0.74 | 78 | empty |
| 4 | 51 | 0.67 | 0.96 | 17 | empty |
| 5 | 626 | 0.67 | 0.76 | 71 | empty |
Interfaces
9 interfaces between chains.
- B–C · 883 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 817 Ų buried · 7 hydrogen bonds · protein-protein
- C–E · 773 Ų buried · 13 hydrogen bonds · protein-protein
- B–F · 766 Ų buried · 9 hydrogen bonds · protein-protein
- D–E · 765 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 2C8N · The Structure of a family 51 arabinofuranosidase, Araf51, from Clostridium thermocellum… · 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 Q4CJG5
- Elsewhere: RCSB PDB 2C8N · PDBe 2C8N · UniProt Q4CJG5
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