MolNFT v1 · #65998 · protein
Crystal structure of full-length endolysin R21 from phage 21
3HDE · Lysozyme: “Crystal structure of full-length endolysin R21 from phage 21”. X-ray diffraction, 5 pockets (best druggability 0.75). MolNFT v1 #65998 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3HDE
- Type
- protein
- Length
- 651 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysozyme
- EC
- 3.2.1.17
- UniProt
- P27359
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 59% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Lysozyme (EC 3.2.1.17) | protein | 165 | 60% helix, 9% strand | P27359 |
| C | Lysozyme (EC 3.2.1.17) | protein | 164 | 57% helix, 10% strand | P27359 |
| D | Lysozyme (EC 3.2.1.17) | protein | 157 | 60% helix, 8% strand | P27359 |
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 807 | 0.75 | 0.79 | 87 | empty |
| 2 | 830 | 0.75 | 0.79 | 73 | empty |
| 3 | 872 | 0.68 | 0.74 | 84 | empty |
| 4 | 150 | 0.47 | 0.77 | 30 | empty |
| 5 | 65 | 0.34 | 0.77 | 19 | empty |
Interfaces
5 interfaces between chains.
- C–D · 839 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 801 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 103 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 84 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 80 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 3HDE · Crystal structure of full-length 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 3HDE · PDBe 3HDE · UniProt P27359
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