Research workbench
Re-refinement of 4DD6; cisplatin coordination chemistry determination at hen egg white lysozyme HIS15
Analyse Re-refinement of 4DD6; cisplatin coordination chemistry determination at hen… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5L3I
- Type
- protein
- Length
- 129 residues
- Chains
- 1
- 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, CL, NH3
- Pockets
- 1 · best druggability 0.34
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysozyme C (EC 3.2.1.17) | protein | 129 | 41% helix, 11% strand | P00698 |
Ligands and binding sites
- PT · Platinum (II) ion · metal · 5 copies · chains A
- NA · Sodium ion · metal · chains A
- CL · Chloride ion · ion · 6 copies · chains A
- NH3 · Ammonia · ion · 3 copies · chains A
- DMS · Dimethyl sulfoxide · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 83 | 0.34 | 0.75 | 20 | DMS |
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5L3I · Re-refinement of 4dd6; cisplatin coordination chemistry determination at hen egg white… · 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 5L3I · PDBe 5L3I · UniProt P00698
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