MolNFT v1 · #165499 · protein
Proteinase K in complex with a "half sandwich"-type RU(II) coordination compound
6TXG: “Proteinase K in complex with a "half sandwich"-type RU(II) coordination compound”. X-ray diffraction, 5 ligands (NYN, TFS, CA), 1 pocket (best druggability 0.36). MolNFT v1 #165499 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6TXG
- Type
- protein
- Length
- 279 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proteinase K
- EC
- 3.4.21.64
- UniProt
- P06873
- Ligands
- NYN, TFS, CA, NA, NO3
- Pockets
- 1 · best druggability 0.36
Structure
x-ray diffraction · 1 distinct chain · 27% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proteinase K (EC 3.4.21.64) | protein | 279 | 27% helix, 24% strand | P06873 |
Ligands and binding sites
- NYN · chlorido(1,2-diaminoethane-k2N,N')(1,4,7-trithiacyclononane-k3S,S',S'')ruthenium(II) trifluoromethanesulfonate · ligand · 2 copies · chains A
- TFS · trifluoromethanesulfonic acid · ligand · chains A
- CA · Calcium ion · metal · chains A
- NA · Sodium ion · metal · chains A
- NO3 · Nitrate ion · ion · 3 copies · chains A
- EDO · 1,2-ethanediol · 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 | 86 | 0.36 | 0.76 | 26 | NO3, EDO |
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6TXG · Proteinase K in complex with a "half sandwich"-type Ru(II) coordination compound · 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 P06873
- Elsewhere: RCSB PDB 6TXG · PDBe 6TXG · UniProt P06873
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