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Crystal structure of aav-sp-II, a glycosylated snake venom serine proteinase from agkistrodon acutus
Analyse Crystal structure of aav-sp-II, a glycosylated snake venom serine proteinase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1OP2
- Type
- protein
- Length
- 234 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Venom serine proteinase
- EC
- 3.4.21.-
- UniProt
- Q9I8X1
- Ligands
- NAG, SO4
- Pockets
- 1 · best druggability 0.41
Structure
x-ray diffraction · 1 distinct chain · 9% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Venom serine proteinase (EC 3.4.21.-) | protein | 234 | 9% helix, 34% strand | Q9I8X1 |
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 | 55 | 0.41 | 0.82 | 15 | empty |
Modifications
Observed in the structure: 6 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 1OP2 · Crystal Structure of AaV-SP-II, a Glycosylated Snake Venom Serine Proteinase from… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9I8X1 · AlphaFold monomer V2.0 prediction for snake venom serine protease dav-pa (Q9I8X1) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q9I8X1
- Elsewhere: RCSB PDB 1OP2 · PDBe 1OP2 · UniProt Q9I8X1
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