Research workbench
Crystal structure of GH121 beta-L-arabinobiosidase HYPBA2 from bifidobacterium longum
Analyse Crystal structure of GH121 beta-L-arabinobiosidase HYPBA2 from bifidobacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6M5A
- Type
- protein
- Length
- 844 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-L-arabinobiosidase
- UniProt
- A0A413AH52
- Ligands
- CA
- Pockets
- 8 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-L-arabinobiosidase | protein | 844 | 31% helix, 23% strand | A0A413AH52 |
Ligands and binding sites
- CA · Calcium ion · metal · 3 copies · chains A
- EDO · 1,2-ethanediol · additive · 10 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · 8 copies · chains A
- PGE · Triethylene glycol · additive · 4 copies · chains A
- PG4 · Tetraethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 405 | 0.69 | 0.81 | 35 | PEG |
| 2 | 323 | 0.64 | 0.80 | 44 | PEG |
| 3 | 165 | 0.63 | 0.85 | 37 | PGE |
| 4 | 156 | 0.55 | 0.81 | 23 | empty |
| 5 | 135 | 0.42 | 0.75 | 19 | empty |
Compared structures
- 6M5A · Crystal structure of GH121 beta-L-arabinobiosidase HypBA2 from Bifidobacterium longum · 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 A0A413AH52
- Elsewhere: RCSB PDB 6M5A · PDBe 6M5A · UniProt A0A413AH52
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