MolNFT v1 · #8189 · protein
The thermostable serine-carboxyl type proteinase, kumamolisin (kscp) - complex with ac-ile-pro-phe-cho
1GTL · Kumamolysin: “The thermostable serine-carboxyl type proteinase, kumamolisin (kscp) - complex with ac-ile-pro-phe-cho”. X-ray diffraction, 3 ligands (ACE, CA, SO4), 8 pockets (best druggability 0.70). MolNFT v1 #8189 on GenesisL1: 3D…
- PDB
- 1GTL
- Type
- protein
- Length
- 720 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Kumamolysin; Aldehyde inhibitor
- Ligands
- ACE, CA, SO4
- Pockets
- 8 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 1, 2 | Kumamolysin | protein | 357 | 28% helix, 24% strand | — |
| 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
8 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 202 | 0.70 | 0.87 | 35 | SO4 |
| 2 | 158 | 0.46 | 0.76 | 27 | empty |
| 3 | 114 | 0.46 | 0.79 | 22 | empty |
| 4 | 124 | 0.37 | 0.73 | 25 | empty |
| 5 | 105 | 0.34 | 0.73 | 22 | empty |
Interfaces
3 interfaces between chains.
- 1–2 · 610 Ų buried · 4 hydrogen bonds · protein-protein
- 2–4 · 299 Ų buried · 10 hydrogen bonds · protein-protein
- 1–3 · 298 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 modified (covalent ligand, nonstandard).
Compared structures
- 1GTL · The thermostable serine-carboxyl type proteinase, kumamolisin (KSCP) - complex with… · 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
- Elsewhere: RCSB PDB 1GTL · PDBe 1GTL
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