Research workbench
Native structure of endo-1,5-alpha-L-arabinanases from bacillus subtilis
Analyse Native structure of endo-1,5-alpha-L-arabinanases from bacillus subtilis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2X8F
- Type
- protein
- Length
- 886 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endo-alpha-1,5-L-arabinanase
- EC
- 3.2.1.99
- UniProt
- B3FRL6
- Ligands
- NA, CA, PO4
- Pockets
- 11 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 5% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Endo-alpha-1,5-L-arabinanase (EC 3.2.1.99) | protein | 443 | 5% helix, 44% strand | B3FRL6 |
Ligands and binding sites
- NA · Sodium ion · metal · 4 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 10 copies · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains B
- MRD · (4R)-2-methylpentane-2,4-diol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 341 | 0.63 | 0.79 | 26 | NA |
| 2 | 308 | 0.61 | 0.79 | 25 | NA |
| 3 | 223 | 0.55 | 0.78 | 28 | empty |
| 4 | 275 | 0.55 | 0.76 | 41 | empty |
| 5 | 210 | 0.50 | 0.76 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 644 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 2X8F · Native structure of Endo-1,5-alpha-L-arabinanases from Bacillus subtilis · 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 B3FRL6
- Elsewhere: RCSB PDB 2X8F · PDBe 2X8F · UniProt B3FRL6
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