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Crystal structure of the thermostable serine-carboxyl type proteinase, kumamolisin (kscp) - complex with ac-ile-ala-phe-cho
Analyse Crystal structure of the thermostable serine-carboxyl type proteinase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1GTJ
- Type
- protein
- Length
- 720 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Kumamolysin; Aldehyde inhibitor
- UniProt
- Q8RR56
- Ligands
- ACE, CA, SO4
- Pockets
- 7 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 1, 2 | Kumamolysin | protein | 357 | 31% helix, 23% strand | Q8RR56 |
| 3, 4 | Aldehyde inhibitor | protein | 3 | 0% helix, 33% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains 1, 3, 2, 4
- CA · Calcium ion · metal · 2 copies · chains 1, 2
- SO4 · Sulfate ion · ion · 2 copies · chains 1, 2
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 307 | 0.69 | 0.83 | 47 | SO4 |
| 2 | 108 | 0.44 | 0.78 | 22 | empty |
| 3 | 85 | 0.34 | 0.75 | 19 | empty |
| 4 | 90 | 0.33 | 0.73 | 17 | empty |
| 5 | 72 | 0.32 | 0.75 | 17 | empty |
Interfaces
3 interfaces between chains.
- 1–2 · 636 Ų buried · 3 hydrogen bonds · protein-protein
- 1–3 · 294 Ų buried · 10 hydrogen bonds · protein-protein
- 2–4 · 291 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 modified (covalent ligand, nonstandard).
Compared structures
- 1GTJ · Crystal structure of the thermostable serine-carboxyl type proteinase, kumamolisin (KSCP)… · the same entry in another collection · chain 1 against 1, 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 Q8RR56
- Elsewhere: RCSB PDB 1GTJ · PDBe 1GTJ · UniProt Q8RR56
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