MolNFT v1 · #97866 · protein
X-ray structure of endolysin from clostridium perfringens phage PHISM101
4KRT · Autolytic lysozyme: “X-ray structure of endolysin from clostridium perfringens phage PHISM101”. X-ray diffraction, 7 pockets (best druggability 0.66). MolNFT v1 #97866 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4KRT
- Type
- protein
- Length
- 689 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Autolytic lysozyme
- EC
- 3.2.1.17
- UniProt
- Q0SPG7
- Pockets
- 7 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 22% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Autolytic lysozyme (EC 3.2.1.17) | protein | 347 | 22% helix, 35% strand | Q0SPG7 |
| B | Autolytic lysozyme (EC 3.2.1.17) | protein | 342 | 21% helix, 36% strand | Q0SPG7 |
Ligands and binding sites
- ACT · Acetate ion · additive · 14 copies · chains A, B
- MLA · Malonic acid · additive · 2 copies · chains A, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 589 | 0.66 | 0.77 | 58 | empty |
| 2 | 276 | 0.52 | 0.75 | 33 | empty |
| 3 | 124 | 0.47 | 0.78 | 21 | EPE |
| 4 | 154 | 0.46 | 0.76 | 21 | ACT |
| 5 | 109 | 0.43 | 0.77 | 20 | MLA |
Interfaces
1 interface between chains.
- A–B · 460 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 4KRT · X-ray structure of endolysin from clostridium perfringens phage phiSM101 · 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 Q0SPG7
- Elsewhere: RCSB PDB 4KRT · PDBe 4KRT · UniProt Q0SPG7
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