Research workbench
Structure of emre-D3 mutant in complex with monobody L10 and tpp
Analyse Structure of emre-D3 mutant in complex with monobody L10 and tpp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7SV9
- Type
- protein
- Length
- 383 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L10 monobody; Multidrug transporter emre
- UniProt
- P23895
- Ligands
- P4P
- Pockets
- 4 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 52% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, D | L10 monobody | protein | 89 | 3% helix, 53% strand | — |
| B | Multidrug transporter emre | protein | 102 | 76% helix, 1% strand | P23895 |
| A | Multidrug transporter emre | protein | 103 | 69% helix, 1% strand | P23895 |
Ligands and binding sites
- P4P · Tetraphenylphosphonium · ligand · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 733 | 0.79 | 0.83 | 57 | P4P |
| 2 | 65 | 0.45 | 0.82 | 17 | empty |
| 3 | 54 | 0.39 | 0.81 | 17 | empty |
| 4 | 71 | 0.31 | 0.73 | 15 | empty |
Interfaces
3 interfaces between chains.
- B–A · 1405 Ų buried · 9 hydrogen bonds · protein-protein
- C–A · 388 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 379 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 7SV9 · Structure of EmrE-D3 mutant in complex with monobody L10 and TPP · the same entry in another collection · chain C against C, TM-score 1.00
- P23895 · AlphaFold monomer V2.0 prediction for multidrug transporter emre (P23895) · a predicted model of the same protein · chain A against A, TM-score 0.86
- 2I68 · Cryo-EM based theoretical model structure of transmembrane domain of the… · a predicted model of the same protein · chain A against A, TM-score 0.64
- 2I68 · Cryo-EM based theoretical model structure of transmembrane domain of the… · a predicted model of the same protein · chain A against A, TM-score 0.64
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 P23895
- Elsewhere: RCSB PDB 7SV9 · PDBe 7SV9 · UniProt P23895
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