MolNFT v1 · #181316 · protein
Crystal structure of GH5_18-E140A from bifidobacterium longum subsp. longum atcc 55813 in complex with MANB1-4GLCNAC
7LR6 · Glycosyl hydrolase BLGH5_18: “Crystal structure of GH5_18-E140A from bifidobacterium longum subsp. longum atcc 55813 in complex with…”. X-ray diffraction, 3 ligands (NAG, BMA, PO4), 13 pockets (best druggability 0.81). MolNFT v1…
- PDB
- 7LR6
- Type
- protein
- Length
- 1,694 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycosyl hydrolase BLGH5_18
- UniProt
- C2GY91
- Ligands
- NAG, BMA, PO4
- Pockets
- 13 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Glycosyl hydrolase BLGH5_18 | protein | 424 | 41% helix, 16% strand | C2GY91 |
| C, D | Glycosyl hydrolase BLGH5_18 | protein | 423 | 40% helix, 15% strand | C2GY91 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B, C, D
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 15 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 299 | 0.81 | 0.92 | 34 | NAG, BMA |
| 2 | 309 | 0.79 | 0.90 | 35 | NAG, BMA |
| 3 | 294 | 0.79 | 0.90 | 35 | NAG, BMA |
| 4 | 306 | 0.78 | 0.89 | 35 | NAG, BMA |
| 5 | 229 | 0.69 | 0.85 | 37 | empty |
Interfaces
2 interfaces between chains.
- A–C · 644 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 474 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 7LR6 · Crystal structure of GH5_18-E140A from Bifidobacterium longum subsp. longum ATCC 55813 in… · 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 C2GY91
- Elsewhere: RCSB PDB 7LR6 · PDBe 7LR6 · UniProt C2GY91
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