Research workbench
Selectivity mechanism of a bacterial homologue of the human drug peptide transporters PEPT1 and PEPT2
Analyse Selectivity mechanism of a bacterial homologue of the human drug peptide… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4TPG
- Type
- protein
- Length
- 921 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- PROTON:OLIGOPEPTIDE symporter pot family; Ala-L-3-br-tyr-ala
- UniProt
- Q8EHE6
- Ligands
- ZN
- Pockets
- 12 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 77% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | PROTON:OLIGOPEPTIDE symporter pot family | protein | 459 | 78% helix, 0% strand | Q8EHE6 |
| E | Ala-L-3-br-tyr-ala | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · chains A, B
- LMT · Dodecyl-beta-D-maltoside · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 789 | 0.75 | 0.79 | 44 | empty |
| 2 | 613 | 0.70 | 0.78 | 36 | empty |
| 3 | 255 | 0.61 | 0.79 | 32 | empty |
| 4 | 193 | 0.53 | 0.78 | 22 | empty |
| 5 | 209 | 0.48 | 0.74 | 30 | ZN |
Interfaces
2 interfaces between chains.
- A–B · 714 Ų buried · 0 hydrogen bonds · protein-protein
- A–E · 415 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (nonstandard).
Compared structures
- 4TPG · Selectivity mechanism of a bacterial homologue of the human drug peptide transporters… · 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 Q8EHE6
- Elsewhere: RCSB PDB 4TPG · PDBe 4TPG · UniProt Q8EHE6
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.