MolNFT v1 · #121209 · protein
Crystal structure of abna, a GH43 extracellular arabinanase from geobacillus stearothermophilus, in complex with arabinopentaose
5HOF: “Crystal structure of abna, a GH43 extracellular arabinanase from geobacillus stearothermophilus, in complex…”. X-ray diffraction, 2 ligands (AHR, CA), 5 pockets (best druggability 0.68). MolNFT v1 #121209 on GenesisL1: 3D structure…
- PDB
- 5HOF
- Type
- protein
- Length
- 803 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Extracellular arabinanase
- UniProt
- B3EYN2
- Ligands
- AHR, CA
- Pockets
- 5 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 6% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Extracellular arabinanase | protein | 803 | 6% helix, 43% strand | B3EYN2 |
Ligands and binding sites
- AHR · alpha-L-arabinofuranose · sugar · 5 copies · chains A
- CA · Calcium ion · metal · 2 copies · chains A
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains A
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 479 | 0.68 | 0.79 | 45 | empty |
| 2 | 115 | 0.53 | 0.82 | 29 | empty |
| 3 | 137 | 0.47 | 0.78 | 20 | TRS, PEG |
| 4 | 152 | 0.46 | 0.77 | 24 | empty |
| 5 | 151 | 0.44 | 0.75 | 24 | empty |
Compared structures
- 5HOF · Crystal structure of AbnA, a GH43 extracellular arabinanase from Geobacillus… · 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 5HOF · PDBe 5HOF · UniProt B3EYN2
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