Research workbench
Crystal structure of a putative lipoprotein (BDI_3050) from parabacteroides distasonis atcc 8503 at 2.70 a resolution
Analyse Crystal structure of a putative lipoprotein (BDI_3050) from parabacteroides… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4FVS
- Type
- protein
- Length
- 1,283 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative lipoprotein
- UniProt
- A6LGE3
- Ligands
- CL
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 4% helix, 61% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, F | Putative lipoprotein | protein | 214 | 4% helix, 61% strand | A6LGE3 |
| E | Putative lipoprotein | protein | 213 | 4% helix, 61% strand | A6LGE3 |
Ligands and binding sites
- CL · Chloride ion · ion · 4 copies · chains C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1137 | 0.83 | 0.84 | 90 | empty |
| 2 | 319 | 0.61 | 0.78 | 48 | CL |
| 3 | 250 | 0.57 | 0.78 | 29 | empty |
| 4 | 233 | 0.55 | 0.78 | 35 | empty |
| 5 | 234 | 0.55 | 0.78 | 35 | empty |
Interfaces
6 interfaces between chains.
- D–E · 1377 Ų buried · 35 hydrogen bonds · protein-protein
- C–E · 837 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 825 Ų buried · 11 hydrogen bonds · protein-protein
- B–E · 456 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 388 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 modified, 6 disulfide (engineered, disulfide).
Compared structures
- 4FVS · Crystal structure of a putative lipoprotein (BDI_3050) from Parabacteroides distasonis… · 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 A6LGE3
- Elsewhere: RCSB PDB 4FVS · PDBe 4FVS · UniProt A6LGE3
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