MolNFT v1 · #65999 · protein
Crystal structure of truncated endolysin R21 from phage 21
3HDF · Lysozyme: “Crystal structure of truncated endolysin R21 from phage 21”. X-ray diffraction, 1 ligand (NO3), 4 pockets (best druggability 0.66). MolNFT v1 #65999 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3HDF
- Type
- protein
- Length
- 265 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysozyme
- EC
- 3.2.1.17
- UniProt
- P27359
- Ligands
- NO3
- Pockets
- 4 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysozyme (EC 3.2.1.17) | protein | 133 | 52% helix, 8% strand | P27359 |
| B | Lysozyme (EC 3.2.1.17) | protein | 132 | 52% helix, 9% strand | P27359 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 310 | 0.66 | 0.82 | 47 | empty |
| 2 | 146 | 0.55 | 0.81 | 24 | empty |
| 3 | 68 | 0.35 | 0.77 | 15 | GOL |
| 4 | 64 | 0.30 | 0.74 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 999 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 3HDF · Crystal structure of truncated endolysin R21 from phage 21 · 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 P27359
- Elsewhere: RCSB PDB 3HDF · PDBe 3HDF · UniProt P27359
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