MolNFT v1 · #37889 · protein
Crystal structure of the E263A nucleophile mutant of bacillus licheniformis endo-beta-1,4-galactanase in complex with galactotriose
2GFT · Glycosyl hydrolase family 53: “Crystal structure of the E263A nucleophile mutant of bacillus licheniformis endo-beta-1,4-galactanase in…”. X-ray diffraction, 2 ligands (GAL, CA), 4 pockets (best druggability 0.67). MolNFT v1 #37889…
- PDB
- 2GFT
- Type
- protein
- Length
- 773 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycosyl hydrolase family 53
- EC
- 3.2.1.89
- Ligands
- GAL, CA
- Pockets
- 4 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycosyl hydrolase family 53 (EC 3.2.1.89) | protein | 386 | 38% helix, 15% strand | — |
| B | Glycosyl hydrolase family 53 (EC 3.2.1.89) | protein | 387 | 38% helix, 15% strand | — |
Ligands and binding sites
- GAL · beta-D-galactopyranose · sugar · 6 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 361 | 0.67 | 0.81 | 38 | GAL |
| 2 | 348 | 0.66 | 0.80 | 37 | GAL |
| 3 | 542 | 0.65 | 0.76 | 55 | empty |
| 4 | 54 | 0.37 | 0.80 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 314 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 2GFT · Crystal structure of the E263A nucleophile mutant of Bacillus licheniformis… · 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
- Elsewhere: RCSB PDB 2GFT · PDBe 2GFT
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