MolNFT v1 · #103810 · protein
Crystal structure of dimethyllysine hen egg-white lysozyme in complex with SCLX4 at 2.2 a resolution
4PRU · Lysozyme C: “Crystal structure of dimethyllysine hen egg-white lysozyme in complex with SCLX4 at 2.2 a resolution”. X-ray diffraction, 1 ligand (T3Y), 3 pockets (best druggability 0.41). MolNFT v1 #103810 on GenesisL1: 3D structure…
- PDB
- 4PRU
- Type
- protein
- Length
- 258 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysozyme C
- EC
- 3.2.1.17
- UniProt
- P00698
- Ligands
- T3Y
- Pockets
- 3 · best druggability 0.41
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Lysozyme C (EC 3.2.1.17) | protein | 129 | 41% helix, 11% strand | P00698 |
Ligands and binding sites
- T3Y · 25,26,27,28-tetrahydroxypentacyclo[19.3.1.1~3,7~.1~9, 13~.1~15,19~]octacosa-1(25),3(28),4,6,9(27),10,12, 15(26),16,18,21,23-dodecaene-5,11,17,23-tetrasulfonic acid · ligand · 4 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 137 | 0.41 | 0.75 | 28 | empty |
| 2 | 71 | 0.29 | 0.73 | 20 | GOL |
| 3 | 55 | 0.28 | 0.74 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 224 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 12 modified, 8 disulfide (methylation, disulfide, nonstandard).
Compared structures
- 4PRU · Crystal structure of dimethyllysine hen egg-white lysozyme in complex with sclx4 at 2.2 A… · 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 P00698
- Elsewhere: RCSB PDB 4PRU · PDBe 4PRU · UniProt P00698
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