Research workbench
Crystal structure of streptomyces caespitosus sermetstatin in complex with bacillus licheniformis subtilisin
Analyse Crystal structure of streptomyces caespitosus sermetstatin in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HX2
- Type
- protein
- Length
- 772 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Kera; Neutral proteinase inhibitor scnpi
- EC
- 3.4.21.62
- UniProt
- Q9FDF2, Q9FDS0
- Ligands
- 1AX, CA, ZN, K, CL, PO4
- Pockets
- 3 · best druggability 0.57
Structure
x-ray diffraction · 3 distinct chains · 27% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Kera (EC 3.4.21.62) | protein | 274 | 30% helix, 21% strand | Q9FDF2 |
| B | Neutral proteinase inhibitor scnpi | protein | 114 | 23% helix, 38% strand | Q9FDS0 |
| D | Neutral proteinase inhibitor scnpi | protein | 110 | 24% helix, 39% strand | Q9FDS0 |
Ligands and binding sites
- 1AX · (2R,2'R)-3,3'-oxydipropane-1,2-diol · ligand · chains A
- CA · Calcium ion · metal · 4 copies · chains A, C
- ZN · Zinc ion · metal · 2 copies · chains A, B
- K · Potassium ion · metal · 2 copies · chains B
- CL · Chloride ion · ion · chains A
- PO4 · Phosphate ion · ion · chains A
- IPA · Isopropyl alcohol · additive · 3 copies · chains A, C, D
- GOL · Glycerol · additive · 2 copies · chains A, C
- CAC · Cacodylate ion · additive · chains B
- ACT · Acetate ion · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 229 | 0.57 | 0.79 | 37 | K |
| 2 | 178 | 0.54 | 0.80 | 34 | IPA |
| 3 | 79 | 0.36 | 0.77 | 22 | empty |
Interfaces
3 interfaces between chains.
- B–D · 804 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 699 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 671 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 4HX2 · Crystal structure of Streptomyces caespitosus sermetstatin in complex with Bacillus… · 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 Q9FDF2
- Every structure of UniProt Q9FDS0
- Elsewhere: RCSB PDB 4HX2 · PDBe 4HX2 · UniProt Q9FDF2 · UniProt Q9FDS0
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