Research workbench
Ligand binding domain of pseudomonas aeruginosa PAO1 amino acid chemorecpetor pctc in complex with GABA
Analyse Ligand binding domain of pseudomonas aeruginosa PAO1 amino acid chemorecpetor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LTV
- Type
- protein
- Length
- 1,516 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chemotactic transducer pctc
- UniProt
- A0A080VJ62
- Ligands
- ABU, SO4
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · 7 distinct chains · 36% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chemotactic transducer pctc | protein | 215 | 35% helix, 29% strand | A0A080VJ62 |
| B | Chemotactic transducer pctc | protein | 209 | 35% helix, 29% strand | A0A080VJ62 |
| C | Chemotactic transducer pctc | protein | 223 | 36% helix, 30% strand | A0A080VJ62 |
| D | Chemotactic transducer pctc | protein | 226 | 35% helix, 31% strand | A0A080VJ62 |
| E | Chemotactic transducer pctc | protein | 224 | 36% helix, 31% strand | A0A080VJ62 |
| F | Chemotactic transducer pctc | protein | 219 | 36% helix, 31% strand | A0A080VJ62 |
| G | Chemotactic transducer pctc | protein | 200 | 38% helix, 26% strand | A0A080VJ62 |
Ligands and binding sites
- ABU · Gamma-amino-butanoic acid · ligand · 5 copies · chains A, B, C, D, E, F
- SO4 · Sulfate ion · ion · 13 copies · chains A, C, B, E, D, F, G
- ACT · Acetate ion · additive · 6 copies · chains B, C, E, F
- GOL · Glycerol · additive · 3 copies · chains A, C, F, G
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 | 568 | 0.73 | 0.81 | 61 | SO4 |
| 2 | 480 | 0.71 | 0.81 | 60 | SO4 |
| 3 | 484 | 0.62 | 0.75 | 44 | empty |
| 4 | 282 | 0.58 | 0.78 | 42 | empty |
| 5 | 244 | 0.55 | 0.77 | 25 | ABU |
Interfaces
10 interfaces between chains.
- D–F · 1484 Ų buried · 28 hydrogen bonds · protein-protein
- A–C · 1342 Ų buried · 23 hydrogen bonds · protein-protein
- B–E · 1294 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 908 Ų buried · 8 hydrogen bonds · protein-protein
- E–F · 898 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 5LTV · Ligand binding domain of pseudomonas aeruginosa PAO1 amino acid chemorecpetor pctc in… · 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 A0A080VJ62
- Elsewhere: RCSB PDB 5LTV · PDBe 5LTV · UniProt A0A080VJ62
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