MolNFT v1 · #150268 · protein
X-ray structure of the adduct formed upon reaction of lysozyme with a PD(II) complex bearing N,N-pyridylbenzimidazole derivative with an alkylated triphenylphosphonium cation
6GOI · Lysozyme C: “X-ray structure of the adduct formed upon reaction of lysozyme with a PD(II) complex bearing…”. X-ray diffraction, 3 ligands (PD, NO3, CL), 1 pocket (best druggability 0.33). MolNFT v1 #150268 on GenesisL1: 3D…
- PDB
- 6GOI
- 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
- PD, NO3, CL
- Pockets
- 1 · best druggability 0.33
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
- PD · Palladium ion · metal · 2 copies · chains A
- NO3 · Nitrate ion · ion · 6 copies · chains A
- CL · Chloride ion · ion · 2 copies · chains A
- DMS · Dimethyl sulfoxide · additive · 2 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 | 71 | 0.33 | 0.75 | 16 | NO3, DMS |
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6GOI · X-ray structure of the adduct formed upon reaction of lysozyme with a Pd(II) complex… · 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 6GOI · PDBe 6GOI · UniProt P00698
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