Research workbench
Crystal structure of putative adhesin (YP_001304413.1) from parabacteroides distasonis atcc 8503 at 2.41 a resolution
Analyse Crystal structure of putative adhesin (YP_001304413.1) from parabacteroides… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LJY
- Type
- protein
- Length
- 716 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative adhesin
- UniProt
- A6LGH7
- Ligands
- CL
- Pockets
- 2 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 3% helix, 66% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Putative adhesin | protein | 239 | 3% helix, 66% strand | A6LGH7 |
| B | Putative adhesin | protein | 238 | 3% helix, 66% strand | A6LGH7 |
Ligands and binding sites
- CL · Chloride ion · ion · chains C
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains B, A, C
- PGE · Triethylene glycol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 922 | 0.77 | 0.80 | 94 | PEG |
| 2 | 84 | 0.36 | 0.76 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–B · 591 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 231 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 180 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (engineered).
Compared structures
- 3LJY · Crystal structure of putative adhesin (YP_001304413.1) 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 A6LGH7
- Elsewhere: RCSB PDB 3LJY · PDBe 3LJY · UniProt A6LGH7
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