MolNFT v1 · #87076 · protein
Structural analysis of an exo-beta-agarase
4BQ2 · B-agarase: “Structural analysis of an exo-beta-agarase”. X-ray diffraction, 1 ligand (CA), 20 pockets (best druggability 0.78). MolNFT v1 #87076 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4BQ2
- Type
- protein
- Length
- 2,967 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- B-agarase
- EC
- 3.2.1.81
- UniProt
- Q21HC5
- Ligands
- CA
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 27% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | B-agarase (EC 3.2.1.81) | protein | 746 | 28% helix, 23% strand | Q21HC5 |
| B | B-agarase (EC 3.2.1.81) | protein | 747 | 26% helix, 24% strand | Q21HC5 |
| C | B-agarase (EC 3.2.1.81) | protein | 748 | 27% helix, 23% strand | Q21HC5 |
| D | B-agarase (EC 3.2.1.81) | protein | 726 | 27% helix, 23% strand | Q21HC5 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 22 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 900 | 0.78 | 0.80 | 95 | GOL |
| 2 | 855 | 0.78 | 0.81 | 94 | GOL |
| 3 | 895 | 0.78 | 0.80 | 95 | GOL |
| 4 | 734 | 0.76 | 0.80 | 80 | GOL |
| 5 | 69 | 0.75 | 0.99 | 26 | GOL |
Interfaces
4 interfaces between chains.
- A–C · 491 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 383 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 333 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 203 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4BQ2 · 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 4BQ2 · PDBe 4BQ2 · UniProt Q21HC5
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