MolNFT v1 · #126401 · protein
The case of 1LKR held at the pdb and its variable amino acid occupancies; re refinement of 4OW9 to correct this
5M1Y · Lysozyme C: “The case of 1LKR held at the pdb and its variable amino acid occupancies; re refinement of 4OW9 to correct…”. X-ray diffraction, 4 ligands (PT, NA, IOD), 2 pockets (best druggability 0.35). MolNFT v1 #126401 on…
- PDB
- 5M1Y
- 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
- PT, NA, IOD, CL
- Pockets
- 2 · best druggability 0.35
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Lysozyme C (EC 3.2.1.17) | protein | 129 | 40% helix, 12% strand | P00698 |
Ligands and binding sites
- PT · Platinum (II) ion · metal · 3 copies · chains A, B
- NA · Sodium ion · metal · chains B
- IOD · Iodide ion · ion · 26 copies · chains A, B
- CL · Chloride ion · ion · 3 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 71 | 0.35 | 0.76 | 19 | DMS |
| 2 | 60 | 0.32 | 0.76 | 18 | DMS |
Interfaces
1 interface between chains.
- A–B · 284 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 5M1Y · The case of 1lkr held at the PDB and its variable amino acid occupancies; re refinement… · 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 5M1Y · PDBe 5M1Y · UniProt P00698
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