Research workbench
High pressure protein crystallography of hen egg white lysozyme at 950 mpa
Analyse High pressure protein crystallography of hen egg white lysozyme at 950 mpa in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4WM6
- Type
- protein
- Length
- 516 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysozyme C
- EC
- 3.2.1.17
- UniProt
- P00698
- Ligands
- NA
- Pockets
- 6 · best druggability 0.62
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Lysozyme C (EC 3.2.1.17) | protein | 129 | 40% helix, 11% strand | P00698 |
Ligands and binding sites
- NA · Sodium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 403 | 0.62 | 0.77 | 58 | empty |
| 2 | 369 | 0.55 | 0.74 | 43 | empty |
| 3 | 132 | 0.45 | 0.78 | 25 | empty |
| 4 | 112 | 0.35 | 0.74 | 17 | empty |
| 5 | 79 | 0.33 | 0.74 | 22 | empty |
Interfaces
4 interfaces between chains.
- A–D · 380 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 335 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 58 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 12 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 4WM6 · High pressure protein crystallography of hen egg white lysozyme at 950 MPa · 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 4WM6 · PDBe 4WM6 · UniProt P00698
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