Research workbench
Crystal structure of the protein Q88SR8 from lactobacillus plantarum. northeast structural genomics consortium target LPR109.
Analyse Crystal structure of the protein Q88SR8 from lactobacillus plantarum. northeast… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DC7
- Type
- protein
- Length
- 630 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative uncharacterized protein LP_3323
- UniProt
- Q88SR8
- Ligands
- NA, MG, SO4
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative uncharacterized protein LP_3323 | protein | 213 | 39% helix, 13% strand | Q88SR8 |
| B | Putative uncharacterized protein LP_3323 | protein | 209 | 38% helix, 13% strand | Q88SR8 |
| C | Putative uncharacterized protein LP_3323 | protein | 208 | 38% helix, 13% strand | Q88SR8 |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains B, A, C
- MG · Magnesium ion · metal · chains B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1095 | 0.78 | 0.80 | 72 | SO4, NA |
| 2 | 86 | 0.58 | 0.87 | 24 | empty |
| 3 | 132 | 0.52 | 0.81 | 25 | empty |
| 4 | 123 | 0.50 | 0.80 | 20 | empty |
| 5 | 175 | 0.48 | 0.76 | 22 | empty |
Interfaces
3 interfaces between chains.
- A–B · 885 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 866 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 812 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 modified (engineered).
Compared structures
- 3DC7 · Crystal structure of the protein Q88SR8 from Lactobacillus plantarum. Northeast… · 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 Q88SR8
- Elsewhere: RCSB PDB 3DC7 · PDBe 3DC7 · UniProt Q88SR8
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