Research workbench
Muramidase domain of SpmX from Asticaccaulis excentricus
Analyse Muramidase domain of SpmX from Asticaccaulis excentricus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6H9D
- Type
- protein
- Length
- 443 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.9
- Source
- Asticcacaulis excentricus
- Molecule
- Lysozyme
- EC
- 3.2.1.17
- UniProt
- E8RMG8
- Ligands
- CL
- Pockets
- 3 · best druggability 0.79
Structure
x-ray diffraction · resolution 1.9 · 2 distinct chains · 56% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Lysozyme (EC 3.2.1.17) | protein | 148 | 55% helix, 14% strand | E8RMG8 |
| C | Lysozyme (EC 3.2.1.17) | protein | 147 | 56% helix, 14% strand | E8RMG8 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 985 | 0.79 | 0.81 | 83 | GOL |
| 2 | 373 | 0.65 | 0.79 | 40 | GOL |
| 3 | 120 | 0.53 | 0.82 | 24 | empty |
Interfaces
3 interfaces between chains.
- A–B · 559 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 523 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 483 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6H9D · Muramidase domain of spmx from asticaccaulis excentricus · 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 E8RMG8
- Elsewhere: RCSB PDB 6H9D · PDBe 6H9D · UniProt E8RMG8
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