MolNFT v1 · #61122 · protein
Crystal structure of the protein Q88SR8 from lactobacillus plantarum. northeast structural genomics consortium target LPR109.
3DC7 · Putative uncharacterized protein LP_3323: “Crystal structure of the protein Q88SR8 from lactobacillus plantarum. northeast structural genomics…”. X-ray diffraction, 3 ligands (NA, MG, SO4), 7 pockets (best druggability 0.78). MolNFT…
- 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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