MolNFT v1 · #164219 · protein
Insights into a novel NLPC/P60 endopeptidase from photobacterium damselae subsp. piscicida
6SQX · Peptide-binding protein: “Insights into a novel NLPC/P60 endopeptidase from photobacterium damselae subsp. piscicida”. X-ray diffraction, 2 ligands (BCT, CL), 12 pockets (best druggability 0.84). MolNFT v1 #164219 on GenesisL1: 3D…
- PDB
- 6SQX
- Type
- protein
- Length
- 914 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptide-binding protein
- UniProt
- A0A1V1VDL8
- Ligands
- BCT, CL
- Pockets
- 12 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptide-binding protein | protein | 457 | 27% helix, 29% strand | A0A1V1VDL8 |
| B | Peptide-binding protein | protein | 457 | 26% helix, 29% strand | A0A1V1VDL8 |
Ligands and binding sites
- BCT · Bicarbonate ion · ligand · chains B
- CL · Chloride ion · ion · 6 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 38 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 225 | 0.84 | 0.96 | 51 | empty |
| 2 | 923 | 0.79 | 0.81 | 89 | EDO |
| 3 | 66 | 0.74 | 0.99 | 19 | CL |
| 4 | 65 | 0.74 | 0.99 | 19 | CL |
| 5 | 766 | 0.73 | 0.79 | 69 | EDO |
Interfaces
1 interface between chains.
- A–B · 2189 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide, 2 modified (disulfide, oxidation).
Compared structures
- 6SQX · Insights into a novel NlpC/P60 Endopeptidase from Photobacterium damselae subsp. piscicida · 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 A0A1V1VDL8
- Elsewhere: RCSB PDB 6SQX · PDBe 6SQX · UniProt A0A1V1VDL8
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