Research workbench
Crystal structure of putative lipid binding protein (YP_001304415.1) from parabacteroides distasonis atcc 8503 at 2.16 a resolution
Analyse Crystal structure of putative lipid binding protein (YP_001304415.1) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3JX8
- Type
- protein
- Length
- 1,481 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative lipoprotein
- UniProt
- A6LGH9
- Ligands
- SO4, CL
- Pockets
- 16 · best druggability 0.57
Structure
x-ray diffraction · 2 distinct chains · 2% helix, 67% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, E, F | Putative lipoprotein | protein | 247 | 2% helix, 67% strand | A6LGH9 |
| D | Putative lipoprotein | protein | 246 | 2% helix, 67% strand | A6LGH9 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 20 copies · chains A, B, C, D, E, F
- CL · Chloride ion · ion · chains B
- GOL · Glycerol · additive · 20 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 377 | 0.57 | 0.75 | 42 | empty |
| 2 | 207 | 0.53 | 0.78 | 43 | SO4 |
| 3 | 250 | 0.50 | 0.75 | 31 | empty |
| 4 | 148 | 0.50 | 0.79 | 28 | SO4 |
| 5 | 132 | 0.48 | 0.79 | 29 | SO4 |
Interfaces
6 interfaces between chains.
- A–B · 1032 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 1023 Ų buried · 6 hydrogen bonds · protein-protein
- E–F · 1023 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 336 Ų buried · 6 hydrogen bonds · protein-protein
- B–E · 313 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (engineered).
Compared structures
- 3JX8 · Crystal structure of Putative lipid binding protein (YP_001304415.1) from Parabacteroides… · 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 A6LGH9
- Elsewhere: RCSB PDB 3JX8 · PDBe 3JX8 · UniProt A6LGH9
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