Research workbench
Crystal structure of GH5_18 from bifidobacterium longum subsp. longum atcc 55813
Analyse Crystal structure of GH5_18 from bifidobacterium longum subsp. longum atcc 55813 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LR1
- Type
- protein
- Length
- 1,684 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycosyl hydrolase BLGH5_18
- UniProt
- C2GY91
- Ligands
- PO4
- Pockets
- 16 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Glycosyl hydrolase BLGH5_18 | protein | 418 | 41% helix, 16% strand | C2GY91 |
| C, D | Glycosyl hydrolase BLGH5_18 | protein | 424 | 40% helix, 16% strand | C2GY91 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 15 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 28 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 204 | 0.83 | 0.97 | 34 | PO4, EDO |
| 2 | 209 | 0.83 | 0.96 | 34 | PO4, EDO |
| 3 | 1158 | 0.75 | 0.78 | 106 | EDO, PO4 |
| 4 | 185 | 0.69 | 0.87 | 36 | empty |
| 5 | 372 | 0.69 | 0.81 | 33 | EDO |
Interfaces
4 interfaces between chains.
- B–D · 1772 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 1765 Ų buried · 29 hydrogen bonds · protein-protein
- B–C · 571 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 550 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 7LR1 · Crystal structure of GH5_18 from Bifidobacterium longum subsp. longum ATCC 55813 · 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 7LR1 · PDBe 7LR1 · UniProt C2GY91
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