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Crystal structure of GH5_18-E153A from streptomyces cattleya in complex with MANB1-4GLCNAC
Analyse Crystal structure of GH5_18-E153A from streptomyces cattleya in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LR8
- Type
- protein
- Length
- 828 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein SCGH5_18
- UniProt
- F8JJ04
- Ligands
- AE3, NAG, BMA, SO4
- Pockets
- 8 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized protein SCGH5_18 | protein | 413 | 42% helix, 15% strand | F8JJ04 |
| B | Uncharacterized protein SCGH5_18 | protein | 415 | 44% helix, 15% strand | F8JJ04 |
Ligands and binding sites
- AE3 · 2-(2-ethoxyethoxy)ethanol · ligand · 3 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains B
- EDO · 1,2-ethanediol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 255 | 0.83 | 0.94 | 45 | empty |
| 2 | 325 | 0.66 | 0.80 | 29 | NAG, BMA, AE3 |
| 3 | 309 | 0.66 | 0.81 | 30 | NAG, BMA |
| 4 | 87 | 0.52 | 0.84 | 24 | empty |
| 5 | 65 | 0.49 | 0.85 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1536 Ų buried · 36 hydrogen bonds · protein-protein
Compared structures
- 7LR8 · Crystal structure of GH5_18-E153A from Streptomyces cattleya in complex with Manb1-4GlcNAc · 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 F8JJ04
- Elsewhere: RCSB PDB 7LR8 · PDBe 7LR8 · UniProt F8JJ04
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