MolNFT v1 · #165938 · protein
Crystal structure of a GH128 (subgroup III) curdlan-specific exo-beta- 1,3-glucanase from blastomyces gilchristii (BGGH128_III) in complex with laminaribiose at -3 and -2 subsites
6UB1 · Glycoside hydrolase: “Crystal structure of a GH128 (subgroup III) curdlan-specific exo-beta- 1,3-glucanase from blastomyces…”. X-ray diffraction, 1 ligand (BGC), 7 pockets (best druggability 0.72). MolNFT v1 #165938 on GenesisL1: 3D…
- PDB
- 6UB1
- Type
- protein
- Length
- 920 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycoside hydrolase
- UniProt
- A0A179UGT5
- Ligands
- BGC
- Pockets
- 7 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Glycoside hydrolase | protein | 230 | 42% helix, 23% strand | A0A179UGT5 |
Ligands and binding sites
- BGC · beta-D-glucopyranose · sugar · 7 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 361 | 0.72 | 0.84 | 66 | empty |
| 2 | 362 | 0.72 | 0.84 | 64 | empty |
| 3 | 192 | 0.62 | 0.83 | 29 | empty |
| 4 | 242 | 0.54 | 0.77 | 38 | BGC |
| 5 | 82 | 0.48 | 0.82 | 21 | BGC |
Interfaces
5 interfaces between chains.
- C–D · 292 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 278 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 264 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 196 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 188 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6UB1 · Crystal structure of a GH128 (subgroup III) curdlan-specific exo-beta-1,3-glucanase from… · 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 A0A179UGT5
- Elsewhere: RCSB PDB 6UB1 · PDBe 6UB1 · UniProt A0A179UGT5
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