MolNFT v1 · #108918 · protein
High pressure protein crystallography of hen egg white lysozyme at 950 mpa
4WM6 · Lysozyme C: “High pressure protein crystallography of hen egg white lysozyme at 950 mpa”. X-ray diffraction, 1 ligand (NA), 6 pockets (best druggability 0.62). MolNFT v1 #108918 on GenesisL1: 3D structure, binding sites and pockets…
- 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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