Research workbench
2.5 ångström crystal structure of putative lipoprotein from clostridium perfringens
Analyse 2.5 ångström crystal structure of putative lipoprotein from clostridium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5J7R
- Type
- protein
- Length
- 581 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative lipoprotein
- UniProt
- A0A0N9KSH4
- Ligands
- MG, CL
- Pockets
- 6 · best druggability 0.61
Structure
x-ray diffraction · 3 distinct chains · 25% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative lipoprotein | protein | 146 | 25% helix, 28% strand | A0A0N9KSH4 |
| B | Putative lipoprotein | protein | 149 | 24% helix, 28% strand | A0A0N9KSH4 |
| C, D | Putative lipoprotein | protein | 143 | 25% helix, 29% strand | A0A0N9KSH4 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, C, D, B
- CL · Chloride ion · ion · chains B
- PEG · Di(hydroxyethyl)ether · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 389 | 0.61 | 0.77 | 36 | empty |
| 2 | 375 | 0.61 | 0.77 | 33 | empty |
| 3 | 104 | 0.44 | 0.79 | 25 | MG |
| 4 | 154 | 0.43 | 0.75 | 28 | MG |
| 5 | 66 | 0.41 | 0.80 | 18 | empty |
Interfaces
5 interfaces between chains.
- C–D · 2316 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 524 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 505 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 269 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 258 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 5J7R · 2.5 Angstrom Crystal Structure of Putative Lipoprotein from Clostridium perfringens · 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 A0A0N9KSH4
- Elsewhere: RCSB PDB 5J7R · PDBe 5J7R · UniProt A0A0N9KSH4
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.