Research workbench
Gly-ser-splb protease from staphylococcus aureus at 1.60 a resolution
Analyse Gly-ser-splb protease from staphylococcus aureus at 1.60 a resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4K1T
- Type
- protein
- Length
- 607 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Serine protease splb
- EC
- 3.4.21.-
- UniProt
- Q2FXC3
- Ligands
- ZN, SO4, CL
- Pockets
- 4 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 12% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Serine protease splb (EC 3.4.21.-) | protein | 202 | 12% helix, 41% strand | Q2FXC3 |
| C | Serine protease splb (EC 3.4.21.-) | protein | 203 | 12% helix, 41% strand | Q2FXC3 |
Ligands and binding sites
- ZN · Zinc ion · metal · 10 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 8 copies · chains A, B, C
- CL · Chloride ion · ion · 3 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 406 | 0.68 | 0.81 | 71 | CL |
| 2 | 164 | 0.45 | 0.76 | 27 | SO4 |
| 3 | 134 | 0.44 | 0.76 | 30 | SO4 |
| 4 | 100 | 0.41 | 0.77 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–C · 550 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 548 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 511 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 4K1T · Gly-Ser-SplB protease from Staphylococcus aureus at 1.60 A resolution · the same entry in another collection · chain A against A, TM-score 1.00
- Q2FXC3 · AlphaFold monomer V2.0 prediction for serine protease splb (Q2FXC3) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 Q2FXC3
- Elsewhere: RCSB PDB 4K1T · PDBe 4K1T · UniProt Q2FXC3
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