Research workbench
Crystal structure of a lysin
Analyse Crystal structure of a lysin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2NW0
- Type
- protein
- Length
- 378 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Plyb
- EC
- 3.2.1.17
- Pockets
- 3 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Plyb (EC 3.2.1.17) | protein | 189 | 30% helix, 29% strand | — |
Ligands and binding sites
- ACT · Acetate ion · additive · 6 copies · chains A, B
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 | 498 | 0.63 | 0.76 | 57 | ACT |
| 2 | 115 | 0.41 | 0.76 | 19 | ACT |
| 3 | 130 | 0.40 | 0.74 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 424 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 2NW0 · Crystal structure of a lysin · 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 2NW0 · PDBe 2NW0
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