Research workbench
Crystal structure of proteinase K inhibited by a lactoferrin octapeptide gly-asp-glu-gln-gly-glu-asn-lys at 2.15 a resolution
Analyse Crystal structure of proteinase K inhibited by a lactoferrin octapeptide… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2HD4
- Type
- protein
- Length
- 287 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proteinase K; 8-mer peptide from lactotransferrin
- EC
- 3.4.21.64, 3.4.21.-
- UniProt
- P06873, Q8TCD2
- Ligands
- CA
- Pockets
- 1 · best druggability 0.48
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proteinase K (EC 3.4.21.64) | protein | 279 | 27% helix, 24% strand | P06873 |
| B | 8-mer peptide from lactotransferrin (EC 3.4.21.-) | protein | 8 | 0% helix, 0% strand | Q8TCD2 |
Ligands and binding sites
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 | 155 | 0.48 | 0.78 | 24 | ACY |
Interfaces
1 interface between chains.
- A–B · 403 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 2HD4 · Crystal structure of proteinase K inhibited by a lactoferrin octapeptide… · 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
- Every structure of UniProt Q8TCD2
- Elsewhere: RCSB PDB 2HD4 · PDBe 2HD4 · UniProt P06873 · UniProt Q8TCD2
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