Research workbench
3D-structure of the modular autolysin lytc from streptococcus pneumoniae in complex with pneummococcal peptidoglycan fragment
Analyse 3D-structure of the modular autolysin lytc from streptococcus pneumoniae in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2WWD
- Type
- protein
- Length
- 434 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 1,4-beta-N-acetylmuramidase
- EC
- 3.2.1.17
- UniProt
- Q9Z4J8
- Ligands
- CHT, MUB, NAG
- Pockets
- 3 · best druggability 0.60
Structure
x-ray diffraction · 1 distinct chain · 16% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 1,4-beta-N-acetylmuramidase (EC 3.2.1.17) | protein | 434 | 16% helix, 38% strand | Q9Z4J8 |
Ligands and binding sites
- CHT · Choline ion · ligand · 7 copies · chains A
- MUB · N-acetyl-alpha-muramic acid · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
- GOL · Glycerol · additive · 7 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 446 | 0.60 | 0.75 | 44 | empty |
| 2 | 64 | 0.39 | 0.79 | 18 | empty |
| 3 | 86 | 0.34 | 0.74 | 21 | NAG |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 2WWD · 3D-structure of the modular autolysin LytC from Streptococcus pneumoniae in complex with… · 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 Q9Z4J8
- Elsewhere: RCSB PDB 2WWD · PDBe 2WWD · UniProt Q9Z4J8
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