MolNFT v1 · #127948 · protein
Bacteroides ovatus mixed linkage glucan pul (mlgul) GH16 in complex with G4G4G3G product
5NBP · Glycosyl hydrolase family 16: “Bacteroides ovatus mixed linkage glucan pul (mlgul) GH16 in complex with G4G4G3G product”. X-ray diffraction, 2 ligands (BGC, CA), 2 pockets (best druggability 0.80). MolNFT v1 #127948 on GenesisL1: 3D…
- PDB
- 5NBP
- Type
- protein
- Length
- 474 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycosyl hydrolase family 16
- UniProt
- A7LY25
- Ligands
- BGC, CA
- Pockets
- 2 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 7% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Glycosyl hydrolase family 16 | protein | 237 | 7% helix, 48% strand | A7LY25 |
Ligands and binding sites
- BGC · beta-D-glucopyranose · sugar · 7 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 897 | 0.80 | 0.82 | 84 | BGC |
| 2 | 257 | 0.53 | 0.76 | 43 | EDO |
Interfaces
1 interface between chains.
- A–B · 739 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 5NBP · Bacteroides ovatus mixed linkage glucan PUL (MLGUL) GH16 in complex with G4G4G3G Product · 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 A7LY25
- Elsewhere: RCSB PDB 5NBP · PDBe 5NBP · UniProt A7LY25
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