Research workbench
Structure of kumamolisin-as complexed with a covalently-bound inhibitor, acipf
Analyse Structure of kumamolisin-as complexed with a covalently-bound inhibitor, acipf in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1SIO
- Type
- protein
- Length
- 1,072 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Kumamolisin-as; ACE-ile-pro-phl peptide inhibitor
- Ligands
- ACE, CA, SO4
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 31% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Kumamolisin-as | protein | 356 | 31% helix, 23% strand | — |
| B | Kumamolisin-as | protein | 355 | 30% helix, 23% strand | — |
| C | Kumamolisin-as | protein | 352 | 32% helix, 23% strand | — |
| D, E, F | ACE-ile-pro-phl peptide inhibitor | protein | 3 | 0% helix, 33% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 3 copies · chains A, D, B, E, C, F
- CA · Calcium ion · metal · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 3 copies · chains A, B, C
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 | 769 | 0.75 | 0.80 | 86 | empty |
| 2 | 212 | 0.61 | 0.81 | 25 | empty |
| 3 | 203 | 0.50 | 0.76 | 39 | empty |
| 4 | 93 | 0.36 | 0.75 | 21 | empty |
| 5 | 77 | 0.31 | 0.74 | 19 | empty |
Interfaces
5 interfaces between chains.
- A–B · 667 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 378 Ų buried · 3 hydrogen bonds · protein-protein
- C–F · 293 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 291 Ų buried · 9 hydrogen bonds · protein-protein
- B–E · 290 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent, 3 modified (covalent ligand, nonstandard).
Compared structures
- 1SIO · Structure of Kumamolisin-As complexed with a covalently-bound inhibitor, AcIPF · 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 1SIO · PDBe 1SIO
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