Research workbench
Crystal structure of the GH51 arabinofuranosidase from xanthomonas axonopodis pv. citri
Analyse Crystal structure of the GH51 arabinofuranosidase from xanthomonas axonopodis… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6D25
- Type
- protein
- Length
- 2,964 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-L-arabinosidase
- UniProt
- Q8PMY9
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 28% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-L-arabinosidase | protein | 497 | 28% helix, 28% strand | Q8PMY9 |
| B, C, D, F | Alpha-L-arabinosidase | protein | 493 | 29% helix, 29% strand | Q8PMY9 |
| E | Alpha-L-arabinosidase | protein | 495 | 28% helix, 28% strand | Q8PMY9 |
Ligands and binding sites
- GOL · Glycerol · 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, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 196 | 0.75 | 0.90 | 30 | empty |
| 2 | 197 | 0.74 | 0.90 | 31 | empty |
| 3 | 188 | 0.74 | 0.90 | 30 | empty |
| 4 | 176 | 0.74 | 0.91 | 33 | empty |
| 5 | 849 | 0.73 | 0.78 | 77 | empty |
Interfaces
11 interfaces between chains.
- A–B · 1014 Ų buried · 21 hydrogen bonds · protein-protein
- D–F · 997 Ų buried · 20 hydrogen bonds · protein-protein
- D–E · 996 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 992 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 989 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 6D25 · Crystal structure of the GH51 arabinofuranosidase from Xanthomonas axonopodis pv. citri · 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 Q8PMY9
- Elsewhere: RCSB PDB 6D25 · PDBe 6D25 · UniProt Q8PMY9
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