Research workbench
Crystal structure of GH9 exo-beta-D-glucosaminidase PBPRA0520
Analyse Crystal structure of GH9 exo-beta-D-glucosaminidase PBPRA0520 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5DGQ
- Type
- protein
- Length
- 1,151 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative endoglucanase-related protein
- UniProt
- Q6LUT2
- Ligands
- NA
- Pockets
- 10 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative endoglucanase-related protein | protein | 578 | 40% helix, 16% strand | Q6LUT2 |
| B | Putative endoglucanase-related protein | protein | 573 | 40% helix, 16% strand | Q6LUT2 |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 730 | 0.76 | 0.81 | 60 | empty |
| 2 | 73 | 0.74 | 0.98 | 24 | empty |
| 3 | 75 | 0.73 | 0.97 | 25 | empty |
| 4 | 918 | 0.71 | 0.76 | 83 | empty |
| 5 | 212 | 0.67 | 0.85 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 1532 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5DGQ · Crystal structure of GH9 exo-beta-D-glucosaminidase PBPRA0520 · 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 Q6LUT2
- Elsewhere: RCSB PDB 5DGQ · PDBe 5DGQ · UniProt Q6LUT2
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