Research workbench
Triabc transporter from pseudomonas aeruginosa
Analyse Triabc transporter from pseudomonas aeruginosa in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VEJ
- Type
- protein
- Length
- 3,717 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable resistance-nodulation-cell division (rnd) efflux transporter; Probable…
- UniProt
- Q9I6X6, Q9I6X5
- Ligands
- LMU, E2V, PLM
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 2 distinct chains · 43% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Probable resistance-nodulation-cell division (rnd) efflux transporter | protein | 1022 | 51% helix, 15% strand | — |
| P, Q, R | Probable resistance-nodulation-cell division (rnd) efflux membrane fusion PROTEIN,PROBABLE resistance-nodulation-cell division (rnd) efflux membrane fusion protein | protein | 217 | 3% helix, 20% strand | Q9I6X6, Q9I6X5 |
Ligands and binding sites
- LMU · Dodecyl-alpha-D-maltoside · ligand · 3 copies · chains A, B, C
- E2V · (2R)-2-(hexadecanoyloxy)propyl nonadecanoate · ligand · 3 copies · chains A, P, B, Q, C, R
- PLM · Palmitic acid · ligand · 3 copies · chains P, Q, R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 792 | 0.89 | 0.93 | 131 | empty |
| 2 | 1128 | 0.89 | 0.90 | 159 | empty |
| 3 | 967 | 0.89 | 0.91 | 126 | empty |
| 4 | 257 | 0.83 | 0.94 | 47 | empty |
| 5 | 705 | 0.83 | 0.86 | 87 | empty |
Interfaces
12 interfaces between chains.
- B–C · 3007 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 2954 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 2903 Ų buried · 19 hydrogen bonds · protein-protein
- A–P · 2600 Ų buried · 20 hydrogen bonds · protein-protein
- C–R · 2598 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent, 3 lipid (covalent ligand, palmitoylation).
Compared structures
- 6VEJ · TriABC transporter from Pseudomonas aeruginosa · 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 Q9I6X6
- Every structure of UniProt Q9I6X5
- Elsewhere: RCSB PDB 6VEJ · PDBe 6VEJ · UniProt Q9I6X6 · UniProt Q9I6X5
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