MolNFT v1 · #126139 · protein
Ligand binding domain of pseudomonas aeruginosa PAO1 amino acid chemorecpetor pctc in complex with GABA
5LTV · Chemotactic transducer pctc: “Ligand binding domain of pseudomonas aeruginosa PAO1 amino acid chemorecpetor pctc in complex with GABA”. X-ray diffraction, 2 ligands (ABU, SO4), 20 pockets (best druggability 0.73). MolNFT v1 #126139…
- 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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