MolNFT v1 · #40613 · protein
Crystal structure of the modular cpl-1 endolysin complexed with a peptidoglycan analogue (wild-type endolysin)
2IXU · Lysozyme: “Crystal structure of the modular cpl-1 endolysin complexed with a peptidoglycan analogue (wild-type endolysin)”. X-ray diffraction, 2 ligands (MUB, NAG), 4 pockets (best druggability 0.35). MolNFT v1 #40613 on GenesisL1…
- PDB
- 2IXU
- Type
- protein
- Length
- 340 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysozyme
- EC
- 3.2.1.17
- UniProt
- P15057
- Ligands
- MUB, NAG
- Pockets
- 4 · best druggability 0.35
Structure
x-ray diffraction · 1 distinct chain · 19% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysozyme (EC 3.2.1.17) | protein | 340 | 19% helix, 36% strand | P15057 |
Ligands and binding sites
- MUB · N-acetyl-alpha-muramic acid · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
- FMT · Formic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 94 | 0.35 | 0.74 | 22 | empty |
| 2 | 77 | 0.33 | 0.75 | 17 | empty |
| 3 | 67 | 0.32 | 0.75 | 17 | empty |
| 4 | 55 | 0.32 | 0.77 | 14 | empty |
Modifications
Observed in the structure: 1 covalent, 1 modified (covalent ligand, nonstandard).
Compared structures
- 2IXU · Crystal structure of the modular Cpl-1 endolysin complexed with a peptidoglycan analogue… · 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 P15057
- Elsewhere: RCSB PDB 2IXU · PDBe 2IXU · UniProt P15057
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