Research workbench
BPGH86A: a beta-porphyranase of glycoside hydrolase family 86 from the human gut bacterium bacteroides plebeius
Analyse BPGH86A: a beta-porphyranase of glycoside hydrolase family 86 from the human… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4AW7
- Type
- protein
- Length
- 565 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GH86A beta-porphyranase
- EC
- 3.2.1.178
- UniProt
- B5CY96
- Ligands
- L6S, AAL, GAL, GLA, K, CA, IOD, CL
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 22% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GH86A beta-porphyranase (EC 3.2.1.178) | protein | 565 | 22% helix, 37% strand | B5CY96 |
Ligands and binding sites
- L6S · 6-O-sulfo-alpha-L-galactopyranose · ligand · 2 copies · chains A
- AAL · 3,6-anhydro-alpha-L-galactopyranose · ligand · chains A
- GAL · beta-D-galactopyranose · sugar · 3 copies · chains A
- GLA · alpha-D-galactopyranose · sugar · chains A
- K · Potassium ion · metal · 2 copies · chains A
- CA · Calcium ion · metal · chains A
- IOD · Iodide ion · ion · 13 copies · chains A
- CL · Chloride ion · ion · chains A
- EDO · 1,2-ethanediol · 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 | 277 | 0.74 | 0.87 | 31 | empty |
| 2 | 280 | 0.56 | 0.77 | 41 | GLA, L6S, GAL |
| 3 | 79 | 0.42 | 0.80 | 18 | empty |
| 4 | 67 | 0.32 | 0.75 | 20 | empty |
| 5 | 57 | 0.29 | 0.74 | 13 | K |
Modifications
Observed in the structure: 1 glycan (glycosylation).
Compared structures
- 4AW7 · BpGH86A: A beta-porphyranase of glycoside hydrolase family 86 from the human gut… · the same entry in another collection · chain A against A, TM-score 1.00
- B5CY96 · AlphaFold monomer V2.0 prediction for beta-porphyranase a (B5CY96) · a predicted model of the same protein · 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 B5CY96
- Elsewhere: RCSB PDB 4AW7 · PDBe 4AW7 · UniProt B5CY96
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