Research workbench
Bacterial membrane enzyme structure by the in meso method at 2.3 a resolution
Analyse Bacterial membrane enzyme structure by the in meso method at 2.3 a resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RYP
- Type
- protein
- Length
- 164 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lipoprotein signal peptidase
- EC
- 3.4.23.36
- UniProt
- Q6GHN9
- Ligands
- KNH, ZN, SO4
- Pockets
- 2 · best druggability 0.57
Structure
x-ray diffraction · 1 distinct chain · 57% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lipoprotein signal peptidase (EC 3.4.23.36) | protein | 164 | 57% helix, 13% strand | Q6GHN9 |
Ligands and binding sites
- KNH · Myxovirescin A · ligand · chains A
- ZN · Zinc ion · metal · 2 copies · chains A
- SO4 · Sulfate ion · ion · 4 copies · chains A
- OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · 8 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 274 | 0.57 | 0.77 | 34 | KNH |
| 2 | 65 | 0.34 | 0.76 | 11 | OLC |
Compared structures
- 6RYP · Bacterial membrane enzyme structure by the in meso method at 2.3 A resolution · the same entry in another collection · chain A against A, TM-score 1.00
- Q6GHN9 · AlphaFold monomer V2.0 prediction for lipoprotein signal peptidase (Q6GHN9) · a predicted model of the same protein · chain A against A, TM-score 0.93
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 Q6GHN9
- Elsewhere: RCSB PDB 6RYP · PDBe 6RYP · UniProt Q6GHN9
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.