Research workbench
Crystal structure of GH5_18 from bifidobacterium longum subsp. longum atcc 55813 in complex with glcnac
Analyse Crystal structure of GH5_18 from bifidobacterium longum subsp. longum atcc… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LR2
- Type
- protein
- Length
- 1,693 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycosyl hydrolase BLGH5_18
- UniProt
- C2GY91
- Ligands
- NAG, SO4
- Pockets
- 12 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Glycosyl hydrolase BLGH5_18 | protein | 423 | 40% helix, 15% strand | C2GY91 |
| B | Glycosyl hydrolase BLGH5_18 | protein | 424 | 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
- SO4 · Sulfate ion · ion · 10 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 21 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 286 | 0.78 | 0.90 | 34 | NAG, EDO |
| 2 | 283 | 0.76 | 0.88 | 38 | NAG, EDO |
| 3 | 260 | 0.75 | 0.88 | 35 | NAG, EDO |
| 4 | 273 | 0.74 | 0.87 | 34 | EDO, NAG |
| 5 | 578 | 0.69 | 0.78 | 51 | empty |
Interfaces
2 interfaces between chains.
- B–C · 537 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 434 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 7LR2 · Crystal structure of GH5_18 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 7LR2 · PDBe 7LR2 · UniProt C2GY91
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.