Research workbench
Comment on S. W. M. tanley and J. R. helliwell structural dynamics of cisplatin binding to histidine in a protein struct. dyn. 1, 034701 (2014) regarding the refinement of 4MWK, 4MWM, 4MWN and 4OXE and the method we have adopted.
Analyse Comment on S. W. M. tanley and J. R. helliwell structural dynamics of cisplatin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HQ1
- Type
- protein
- Length
- 127 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, NO3, CL
- Pockets
- 1 · best druggability 0.30
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 | 127 | 41% helix, 11% strand | P00698 |
Ligands and binding sites
- PT · Platinum (II) ion · metal · 4 copies · chains A
- NO3 · Nitrate ion · ion · 4 copies · chains A
- CL · Chloride ion · ion · 3 copies · chains A
- DMS · Dimethyl sulfoxide · additive · 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 | 65 | 0.30 | 0.74 | 15 | DMS |
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5HQ1 · Comment on S. W. M. Tanley and J. R. Helliwell Structural dynamics of cisplatin binding… · 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 5HQ1 · PDBe 5HQ1 · UniProt P00698
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