Research workbench
Crystal structure of psychrophilic subtilisin-like serine protease APA1 from antarctic psychrotroph pseudoaleromonas sp. as-11, complexed with inhibitor chymostatin
Analyse Crystal structure of psychrophilic subtilisin-like serine protease APA1 from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1WVM
- Type
- protein
- Length
- 879 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alkaline serine protease; Chymostatin
- EC
- 3.4.21.-
- Ligands
- MG, CA
- Pockets
- 6 · best druggability 0.59
Structure
x-ray diffraction · 3 distinct chains · 23% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alkaline serine protease (EC 3.4.21.-) | protein | 435 | 24% helix, 29% strand | — |
| B | Alkaline serine protease (EC 3.4.21.-) | protein | 436 | 23% helix, 30% strand | — |
| C, D | Chymostatin | protein | 4 | 0% helix, 25% strand | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 8 copies · chains A, B
- CA · Calcium ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 387 | 0.59 | 0.76 | 49 | empty |
| 2 | 271 | 0.51 | 0.74 | 40 | empty |
| 3 | 53 | 0.47 | 0.86 | 16 | empty |
| 4 | 132 | 0.47 | 0.78 | 18 | empty |
| 5 | 54 | 0.32 | 0.77 | 22 | empty |
Interfaces
3 interfaces between chains.
- A–B · 590 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 470 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 463 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 4 modified (disulfide, nonstandard).
Compared structures
- 1WVM · Crystal Structure of Psychrophilic Subtilisin-like Serine Protease APA1 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 1WVM · PDBe 1WVM
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.