Research workbench
Structure of rib domain 'rib long' from lactobacillus acidophilus
Analyse Structure of rib domain 'rib long' from lactobacillus acidophilus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6S5W
- Type
- protein
- Length
- 210 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Surface protein
- UniProt
- Q5FIM8
- Ligands
- NA, SO4
- Pockets
- 2 · best druggability 0.36
Structure
x-ray diffraction · 2 distinct chains · 4% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Surface protein | protein | 106 | 4% helix, 39% strand | Q5FIM8 |
| B | Surface protein | protein | 104 | 4% helix, 41% strand | Q5FIM8 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 105 | 0.36 | 0.74 | 22 | empty |
| 2 | 55 | 0.26 | 0.73 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 519 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 6S5W · Structure of Rib domain 'Rib Long' from Lactobacillus acidophilus · 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 Q5FIM8
- Elsewhere: RCSB PDB 6S5W · PDBe 6S5W · UniProt Q5FIM8
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