Research workbench
Crystal structure of gdx-clo from small multidrug resistance family of transporters in complex with octylguanidinium
Analyse Crystal structure of gdx-clo from small multidrug resistance family of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WK9
- Type
- protein
- Length
- 774 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Multidrug resistance protein, smr family; L10 monobody
- UniProt
- U2EQ00
- Ligands
- U4G
- Pockets
- 3 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A, F, E | Multidrug resistance protein, smr family | protein | 104 | 81% helix, 1% strand | U2EQ00 |
| C, G | L10 monobody | protein | 90 | 3% helix, 53% strand | — |
| D, H | L10 monobody | protein | 89 | 3% helix, 55% strand | — |
Ligands and binding sites
- U4G · N-octylguanidine · ligand · 11 copies · chains B, A, C, F, E, G
- DMU · Decyl-beta-D-maltopyranoside · additive · 4 copies · chains B, A, C, F, E, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 545 | 0.72 | 0.80 | 44 | U4G |
| 2 | 548 | 0.71 | 0.79 | 44 | U4G |
| 3 | 52 | 0.24 | 0.73 | 14 | empty |
Interfaces
7 interfaces between chains.
- B–A · 1375 Ų buried · 13 hydrogen bonds · protein-protein
- F–E · 1361 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 395 Ų buried · 6 hydrogen bonds · protein-protein
- E–G · 382 Ų buried · 6 hydrogen bonds · protein-protein
- F–H · 382 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6WK9 · Crystal structure of Gdx-Clo from Small Multidrug Resistance family of transporters in… · the same entry in another collection · chain C against C, 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 U2EQ00
- Elsewhere: RCSB PDB 6WK9 · PDBe 6WK9 · UniProt U2EQ00
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