MolNFT v1 · #134627 · protein
Crystal structure of BUGH86E322Q in complex with neoagarooctaose
5TA0 · Glycoside hydrolase: “Crystal structure of BUGH86E322Q in complex with neoagarooctaose”. X-ray diffraction, 4 ligands (AAL, GAL, CA), 14 pockets (best druggability 0.78). MolNFT v1 #134627 on GenesisL1: 3D structure, binding sites…
- PDB
- 5TA0
- Type
- protein
- Length
- 1,241 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycoside hydrolase
- Ligands
- AAL, GAL, CA, SO4
- Pockets
- 14 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycoside hydrolase | protein | 626 | 26% helix, 33% strand | — |
| B | Glycoside hydrolase | protein | 615 | 26% helix, 33% strand | — |
Ligands and binding sites
- AAL · 3,6-anhydro-alpha-L-galactopyranose · ligand · 2 copies · chains A
- GAL · beta-D-galactopyranose · sugar · 3 copies · chains A
- CA · Calcium ion · metal · 4 copies · chains A, B
- SO4 · Sulfate ion · ion · 8 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 30 copies · chains A, B
- GOL · Glycerol · additive · 9 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1156 | 0.78 | 0.80 | 131 | SO4, EDO, GOL |
| 2 | 393 | 0.73 | 0.84 | 34 | empty |
| 3 | 389 | 0.73 | 0.84 | 29 | empty |
| 4 | 530 | 0.66 | 0.77 | 52 | AAL, GAL, EDO |
| 5 | 91 | 0.46 | 0.81 | 19 | EDO |
Interfaces
1 interface between chains.
- A–B · 945 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5TA0 · Crystal structure of BuGH86E322Q in complex with neoagarooctaose · 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 5TA0 · PDBe 5TA0
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