Research workbench
Phage-associated cell wall hydrolase plypy from streptococcus pyogenes, space group P6522
Analyse Phage-associated cell wall hydrolase plypy from streptococcus pyogenes, space… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5UDM
- Type
- protein
- Length
- 436 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phage-associated cell wall hydrolase
- UniProt
- A0A0C6FZU1
- Pockets
- 8 · best druggability 0.55
Structure
x-ray diffraction · 2 distinct chains · 15% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Phage-associated cell wall hydrolase | protein | 221 | 15% helix, 46% strand | A0A0C6FZU1 |
| A | Phage-associated cell wall hydrolase | protein | 215 | 15% helix, 46% strand | A0A0C6FZU1 |
Ligands and binding sites
- GOL · Glycerol · additive · 4 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 167 | 0.55 | 0.81 | 27 | empty |
| 2 | 128 | 0.50 | 0.80 | 19 | empty |
| 3 | 91 | 0.45 | 0.80 | 17 | empty |
| 4 | 83 | 0.40 | 0.77 | 17 | GOL |
| 5 | 127 | 0.37 | 0.73 | 19 | empty |
Interfaces
1 interface between chains.
- B–A · 543 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 modified (engineered).
Compared structures
- 5UDM · Phage-associated cell wall hydrolase PlyPy from Streptococcus pyogenes, space group P6522 · the same entry in another collection · chain B against B, 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 A0A0C6FZU1
- Elsewhere: RCSB PDB 5UDM · PDBe 5UDM · UniProt A0A0C6FZU1
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