MolNFT v1 · #134615 · protein
Crystal structure of BUGH2CWT in complex with galactoisofagomine
5T9G · Glycoside hydrolase: “Crystal structure of BUGH2CWT in complex with galactoisofagomine”. X-ray diffraction, 1 ligand (GIF), 20 pockets (best druggability 0.76). MolNFT v1 #134615 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5T9G
- Type
- protein
- Length
- 3,242 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycoside hydrolase
- Ligands
- GIF
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycoside hydrolase | protein | 810 | 17% helix, 38% strand | — |
| B | Glycoside hydrolase | protein | 810 | 16% helix, 38% strand | — |
| C, D | Glycoside hydrolase | protein | 811 | 17% helix, 38% strand | — |
Ligands and binding sites
- GIF · D-galacto-isofagomine · ligand · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 14 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 85 | 0.76 | 0.98 | 25 | empty |
| 2 | 715 | 0.75 | 0.80 | 65 | EDO |
| 3 | 68 | 0.75 | 0.99 | 21 | empty |
| 4 | 75 | 0.75 | 0.98 | 20 | empty |
| 5 | 69 | 0.75 | 0.98 | 19 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1312 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 1256 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 329 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 327 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5T9G · Crystal structure of BuGH2Cwt in complex with Galactoisofagomine · 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 5T9G · PDBe 5T9G
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