Research workbench
Crystal structure of scabies mite inactivated protease paralogue S-D1 (smipp-S-D1)
Analyse Crystal structure of scabies mite inactivated protease paralogue S-D1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3H7T
- Type
- protein
- Length
- 468 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Group 3 allergen smipp-S YVT004A06
- UniProt
- Q6VPT2
- Ligands
- ZN
- Pockets
- 6 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 13% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Group 3 allergen smipp-S YVT004A06 | protein | 235 | 13% helix, 34% strand | Q6VPT2 |
| B | Group 3 allergen smipp-S YVT004A06 | protein | 233 | 13% helix, 33% strand | Q6VPT2 |
Ligands and binding sites
- ZN · Zinc ion · metal · 9 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 56 | 0.67 | 0.96 | 18 | ZN |
| 2 | 337 | 0.60 | 0.78 | 45 | ZN |
| 3 | 132 | 0.60 | 0.85 | 30 | empty |
| 4 | 132 | 0.39 | 0.74 | 19 | empty |
| 5 | 53 | 0.36 | 0.79 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 756 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 3H7T · Crystal structure of scabies mite inactivated protease paralogue S-D1 (SMIPP-S-D1) · 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 Q6VPT2
- Elsewhere: RCSB PDB 3H7T · PDBe 3H7T · UniProt Q6VPT2
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