Research workbench
Crystal structure of BPGH117_E303Q in complex with neoagarobiose
Analyse Crystal structure of BPGH117_E303Q in complex with neoagarobiose in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4AK7
- Type
- protein
- Length
- 742 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Anhydro-alpha-L-galactosidase
- UniProt
- B5CY74
- Ligands
- 47N, MG, CA, CL
- Pockets
- 8 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Anhydro-alpha-L-galactosidase | protein | 369 | 5% helix, 40% strand | B5CY74 |
| B | Anhydro-alpha-L-galactosidase | protein | 373 | 5% helix, 39% strand | B5CY74 |
Ligands and binding sites
- 47N · Neoagarobiose · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- CA · Calcium ion · metal · chains A
- CL · Chloride ion · ion · chains B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A
- ACT · Acetate ion · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 438 | 0.72 | 0.82 | 32 | empty |
| 2 | 416 | 0.68 | 0.80 | 53 | 47N, CL |
| 3 | 418 | 0.68 | 0.80 | 53 | 47N, CA |
| 4 | 153 | 0.55 | 0.81 | 25 | ACT |
| 5 | 146 | 0.50 | 0.79 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 3446 Ų buried · 61 hydrogen bonds · protein-protein
Compared structures
- 4AK7 · Crystal structure of BpGH117_E303Q in complex with neoagarobiose · 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 B5CY74
- Elsewhere: RCSB PDB 4AK7 · PDBe 4AK7 · UniProt B5CY74
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