MolNFT v1 · #87079 · protein
Structural analysis of an exo-beta-agarase
4BQ5 · B-agarase: “Structural analysis of an exo-beta-agarase”. X-ray diffraction, 3 ligands (AAL, GAL, CA), 16 pockets (best druggability 0.79). MolNFT v1 #87079 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4BQ5
- Type
- protein
- Length
- 1,497 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- B-agarase
- EC
- 3.2.1.81
- UniProt
- Q21HC5
- Ligands
- AAL, GAL, CA
- Pockets
- 16 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | B-agarase (EC 3.2.1.81) | protein | 748 | 27% helix, 23% strand | Q21HC5 |
| B | B-agarase (EC 3.2.1.81) | protein | 749 | 26% helix, 23% strand | Q21HC5 |
Ligands and binding sites
- AAL · 3,6-anhydro-alpha-L-galactopyranose · ligand · 8 copies · chains A, B
- GAL · beta-D-galactopyranose · sugar · 8 copies · chains A, B
- CA · Calcium ion · metal · 6 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1176 | 0.79 | 0.81 | 112 | GAL, AAL, GOL |
| 2 | 580 | 0.79 | 0.84 | 54 | GAL, AAL |
| 3 | 68 | 0.75 | 0.99 | 29 | GOL |
| 4 | 295 | 0.66 | 0.82 | 41 | empty |
| 5 | 272 | 0.58 | 0.78 | 34 | empty |
Interfaces
1 interface between chains.
- A–B · 672 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4BQ5 · Structural analysis of an exo-beta-agarase · 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 Q21HC5
- Elsewhere: RCSB PDB 4BQ5 · PDBe 4BQ5 · UniProt Q21HC5
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