Research workbench
Structure of muramidase from trichobolus zukalii
Analyse Structure of muramidase from trichobolus zukalii in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZMV
- Type
- protein
- Length
- 414 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Muramidase
- EC
- 3.2.1.17
- Ligands
- SO4
- Pockets
- 5 · best druggability 0.42
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Muramidase (EC 3.2.1.17) | protein | 207 | 30% helix, 22% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 128 | 0.42 | 0.76 | 23 | empty |
| 2 | 79 | 0.36 | 0.77 | 21 | GOL |
| 3 | 71 | 0.32 | 0.75 | 18 | empty |
| 4 | 72 | 0.32 | 0.75 | 17 | GOL |
| 5 | 84 | 0.32 | 0.73 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 140 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6ZMV · Structure of muramidase from Trichobolus zukalii · 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
- Elsewhere: RCSB PDB 6ZMV · PDBe 6ZMV
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