MolNFT v1 · #182100 · protein
Structure of emre-D3 mutant in complex with monobody L10 and methyl viologen
7MGX · Multidrug transporter emre: “Structure of emre-D3 mutant in complex with monobody L10 and methyl viologen”. X-ray diffraction, 1 ligand (KHJ), 6 pockets (best druggability 0.77). MolNFT v1 #182100 on GenesisL1: 3D structure, binding…
- PDB
- 7MGX
- Type
- protein
- Length
- 760 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Multidrug transporter emre; L10 monobody
- UniProt
- P23895
- Ligands
- KHJ
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 6 distinct chains · 54% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Multidrug transporter emre | protein | 103 | 77% helix, 1% strand | P23895 |
| C, G | L10 monobody | protein | 90 | 3% helix, 49% strand | — |
| E | Multidrug transporter emre | protein | 102 | 72% helix, 1% strand | P23895 |
| B | Multidrug transporter emre | protein | 98 | 76% helix, 0% strand | P23895 |
| D, H | L10 monobody | protein | 89 | 7% helix, 54% strand | — |
| F | Multidrug transporter emre | protein | 99 | 77% helix, 1% strand | P23895 |
Ligands and binding sites
- KHJ · 1,1'-dimethyl-4,4'-bipyridin-1-ium · ligand · 2 copies · chains A, B, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 520 | 0.77 | 0.84 | 38 | KHJ |
| 2 | 717 | 0.77 | 0.81 | 58 | KHJ |
| 3 | 144 | 0.57 | 0.82 | 28 | empty |
| 4 | 117 | 0.55 | 0.83 | 24 | empty |
| 5 | 113 | 0.35 | 0.73 | 25 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1451 Ų buried · 9 hydrogen bonds · protein-protein
- E–F · 1423 Ų buried · 7 hydrogen bonds · protein-protein
- F–H · 396 Ų buried · 7 hydrogen bonds · protein-protein
- E–G · 396 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 393 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 7MGX · Structure of EmrE-D3 mutant in complex with monobody L10 and methyl viologen · 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 E against A, TM-score 0.85
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 7MGX · PDBe 7MGX · UniProt P23895
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