Research workbench
Crystal structure of psychrophilic subtilisin-like serine protease from antarctic psychrotroph pseudoalteromonas sp. as-11 at 0.14 nm resolution
Analyse Crystal structure of psychrophilic subtilisin-like serine protease from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1Y9Z
- Type
- protein
- Length
- 871 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alkaline serine protease
- EC
- 3.4.21.-
- Ligands
- PMS, CA, NA, SO4
- Pockets
- 7 · best druggability 0.50
Structure
x-ray diffraction · 2 distinct chains · 23% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alkaline serine protease (EC 3.4.21.-) | protein | 435 | 23% helix, 29% strand | — |
| B | Alkaline serine protease (EC 3.4.21.-) | protein | 436 | 22% helix, 29% strand | — |
Ligands and binding sites
- PMS · phenylmethanesulfonic acid · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 4 copies · chains A, B
- NA · Sodium ion · metal · 4 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 194 | 0.50 | 0.77 | 40 | empty |
| 2 | 63 | 0.49 | 0.85 | 20 | empty |
| 3 | 105 | 0.41 | 0.77 | 19 | empty |
| 4 | 52 | 0.34 | 0.78 | 24 | empty |
| 5 | 73 | 0.30 | 0.73 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 592 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 covalent (disulfide, covalent ligand).
Compared structures
- 1Y9Z · Crystal Structure of Psychrophilic Subtilisin-like Serine Protease from Antarctic… · 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
- Elsewhere: RCSB PDB 1Y9Z · PDBe 1Y9Z
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.