Research workbench
3-formylrifamycin sv binding to the access pocket of acrb L protomer
Analyse 3-formylrifamycin sv binding to the access pocket of acrb L protomer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZOB
- Type
- protein
- Length
- 3,410 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- UniProt
- P31224
- Ligands
- ETE, 3YI, DDR, DDQ, D10, CL
Structure
x-ray diffraction · 4 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | — | protein | 1035 | — | P31224 |
| B | — | protein | 1034 | — | P31224 |
| C | — | protein | 1033 | — | P31224 |
| D, E | — | protein | 154 | — | — |
Ligands and binding sites
- ETE · 2-{2-[2-2-(methoxy-ethoxy)-ethoxy]-ethoxy}-ethanol · ligand · chains A
- 3YI · (2S,12Z,14E,16S,17S,18R,19R,20R,21S,22R,23S,24E)-8-formyl-5,6,9,17,19-pentahydroxy-23-methoxy-2,4,12,16, 18,20,22-heptamethyl-1,11-dioxo-1,2-dihydro-2,7-(epoxypentadeca[1,11,13]trienoimino)naphtho[2,1-b]furan-21-yl acetate · ligand · chains A
- DDR · (2S)-3-hydroxypropane-1,2-diyl didecanoate · ligand · chains B
- DDQ · Decylamine-N,N-dimethyl-N-oxide · ligand · chains A, B
- D10 · Decane · ligand · chains B, C
- CL · Chloride ion · ion · chains C
- LMT · Dodecyl-beta-D-maltoside · additive · 6 copies · chains A, C, B
- GOL · Glycerol · additive · 4 copies · chains A, C, B, D
- HEX · Hexane · additive · chains A
- EDO · 1,2-ethanediol · additive · chains A, E
- OCT · N-octane · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Compared structures
- 6ZOB · 3-Formylrifamycin SV binding to the access pocket of AcrB L protomer · 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 6ZOB · PDBe 6ZOB · UniProt P31224
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