Research workbench
Crystal structure of the periplasmic binding protein mota in complex with dfg from a. tumefaciens B6
Analyse Crystal structure of the periplasmic binding protein mota in complex with dfg… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5L9I
- Type
- protein
- Length
- 651 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Periplasmic binding protein
- UniProt
- A0A109C781
- Ligands
- SNW, CA
- Pockets
- 6 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Periplasmic binding protein | protein | 326 | 44% helix, 20% strand | A0A109C781 |
| B | Periplasmic binding protein | protein | 325 | 44% helix, 20% strand | A0A109C781 |
Ligands and binding sites
- SNW · Deoxyfructosylglutamine · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 3 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 170 | 0.80 | 0.96 | 41 | SNW, CA |
| 2 | 146 | 0.80 | 0.96 | 34 | SNW |
| 3 | 86 | 0.44 | 0.80 | 17 | empty |
| 4 | 66 | 0.42 | 0.81 | 17 | empty |
| 5 | 67 | 0.33 | 0.76 | 21 | PEG, CA |
Interfaces
1 interface between chains.
- A–B · 84 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5L9I · Crystal structure of the periplasmic binding protein MotA in complex with DFG from A.… · 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 A0A109C781
- Elsewhere: RCSB PDB 5L9I · PDBe 5L9I · UniProt A0A109C781
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