Research workbench
Structure of truncated abna (domains 1-3), a GH43 arabinanase from geobacilllus stearothermophilus, in complex with arabinooctaose
Analyse Structure of truncated abna (domains 1-3), a GH43 arabinanase from geobacilllus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HO9
- Type
- protein
- Length
- 1,192 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Extracellular arabinanase
- UniProt
- B3EYN2
- Ligands
- AHR, SO4
- Pockets
- 10 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 6% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Extracellular arabinanase | protein | 596 | 6% helix, 44% strand | B3EYN2 |
Ligands and binding sites
- AHR · alpha-L-arabinofuranose · sugar · 16 copies · chains A, B
- SO4 · Sulfate ion · ion · 20 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 9 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 583 | 0.70 | 0.79 | 74 | AHR |
| 2 | 559 | 0.70 | 0.79 | 60 | AHR |
| 3 | 415 | 0.64 | 0.77 | 40 | empty |
| 4 | 409 | 0.61 | 0.76 | 36 | empty |
| 5 | 91 | 0.60 | 0.88 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 954 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5HO9 · Structure of truncated AbnA (domains 1-3), a GH43 arabinanase from Geobacilllus… · 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 B3EYN2
- Elsewhere: RCSB PDB 5HO9 · PDBe 5HO9 · UniProt B3EYN2
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