MolNFT v1 · #172010 · protein
Minocycline binding to the deep binding pocket of acrb-G621P
6ZO8: “Minocycline binding to the deep binding pocket of acrb-G621P”. X-ray diffraction, 12 ligands (D10, D12, C14). MolNFT v1 #172010 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6ZO8
- Type
- protein
- Length
- 3,421 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- UniProt
- P31224
- Ligands
- D10, D12, C14, PTY, LPX, MIY, LMU, DDR, DDQ, NA, SO4, CL
Structure
x-ray diffraction · 5 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | — | protein | 1042 | — | P31224 |
| B | — | protein | 1034 | — | P31224 |
| C | — | protein | 1035 | — | P31224 |
| D | — | protein | 156 | — | — |
| E | — | protein | 154 | — | — |
Ligands and binding sites
- D10 · Decane · ligand · 7 copies · chains A, B, C
- D12 · Dodecane · ligand · 3 copies · chains B, A, C
- C14 · Tetradecane · ligand · 2 copies · chains A, B, C
- PTY · Phosphatidylethanolamine · ligand · 2 copies · chains A, B, C
- LPX · (2S)-3-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-hydroxypropyl hexadecanoate · ligand · 2 copies · chains C, B
- MIY · (4s,4as,5ar,12as)-4,7-bis(dimethylamino)-3,10,12,12A-tetrahydroxy-1,11-dioxo-1,4,4A,5,5A,6,11,12A-octahydrotetracene-2-carboxamide · ligand · chains B
- LMU · Dodecyl-alpha-D-maltoside · ligand · chains B
- DDR · (2S)-3-hydroxypropane-1,2-diyl didecanoate · ligand · chains B
- DDQ · Decylamine-N,N-dimethyl-N-oxide · ligand · chains B
- NA · Sodium ion · metal · chains B
- SO4 · Sulfate ion · ion · 3 copies · chains B, C
- CL · Chloride ion · ion · chains B
- GOL · Glycerol · additive · 16 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · 12 copies · chains A, C, B, D, E
- LMT · Dodecyl-beta-D-maltoside · additive · 9 copies · chains A, C, B
- OCT · N-octane · additive · 3 copies · chains B, C
- HEX · Hexane · additive · 3 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Compared structures
- 6ZO8 · Minocycline binding to the deep binding pocket of AcrB-G621P · the same entry in another collection · chain E against E, TM-score 1.00
- P31224 · AlphaFold monomer V2.0 prediction for multidrug efflux pump subunit acrb (P31224) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 P31224
- Elsewhere: RCSB PDB 6ZO8 · PDBe 6ZO8 · UniProt P31224
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