Research workbench
Structure of plyl
Analyse Structure of plyl in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1YB0
- Type
- protein
- Length
- 473 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prophage LAMBDABA02, N-acetylmuramoyl-L-alanine amidase, family 2
- UniProt
- Q81WA9
- Ligands
- ZN, PO4
- Pockets
- 2 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Prophage LAMBDABA02, N-acetylmuramoyl-L-alanine amidase, family 2 | protein | 157 | 42% helix, 17% strand | Q81WA9 |
| B | Prophage LAMBDABA02, N-acetylmuramoyl-L-alanine amidase, family 2 | protein | 159 | 42% helix, 16% strand | Q81WA9 |
Ligands and binding sites
- ZN · Zinc ion · metal · 3 copies · chains A, B, C
- PO4 · Phosphate ion · ion · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 607 | 0.66 | 0.76 | 77 | ZN, PO4 |
| 2 | 251 | 0.55 | 0.77 | 31 | ZN, PO4 |
Interfaces
3 interfaces between chains.
- A–B · 372 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 355 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 341 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 1YB0 · Structure of PlyL · 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 Q81WA9
- Elsewhere: RCSB PDB 1YB0 · PDBe 1YB0 · UniProt Q81WA9
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