Research workbench
3-formylrifamycin sv binding to the access pocket of acrb-G619P_G621P L and T protomers
Analyse 3-formylrifamycin sv binding to the access pocket of acrb-G619P_G621P L and T… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZOH
- Type
- protein
- Length
- 3,408 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Multidrug efflux pump subunit acrb; Darpin
- UniProt
- P31224
- Ligands
- D12, DDQ, 3YI, DDR, PTY, D10, LPX
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 4 distinct chains · 54% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Multidrug efflux pump subunit acrb | protein | 1034 | 54% helix, 19% strand | P31224 |
| C | Multidrug efflux pump subunit acrb | protein | 1033 | 54% helix, 19% strand | P31224 |
| D | Darpin | protein | 154 | 54% helix, 0% strand | — |
| E | Darpin | protein | 153 | 54% helix, 0% strand | — |
Ligands and binding sites
- D12 · Dodecane · ligand · 4 copies · chains A, B, C
- DDQ · Decylamine-N,N-dimethyl-N-oxide · ligand · 2 copies · chains A, B
- 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 · 2 copies · chains A, B
- DDR · (2S)-3-hydroxypropane-1,2-diyl didecanoate · ligand · chains B
- PTY · Phosphatidylethanolamine · ligand · chains B, C
- D10 · Decane · ligand · chains C
- LPX · (2S)-3-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-hydroxypropyl hexadecanoate · ligand · chains C
- EDO · 1,2-ethanediol · additive · 10 copies · chains A, B, C, D
- LMT · Dodecyl-beta-D-maltoside · additive · 7 copies · chains A, C, B
- GOL · Glycerol · additive · 4 copies · chains A, C, B
- HEX · Hexane · additive · 2 copies · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 958 | 0.88 | 0.90 | 119 | EDO, GOL |
| 2 | 1198 | 0.87 | 0.88 | 134 | empty |
| 3 | 558 | 0.87 | 0.92 | 76 | EDO |
| 4 | 1159 | 0.84 | 0.85 | 116 | empty |
| 5 | 1145 | 0.82 | 0.83 | 99 | EDO |
Interfaces
7 interfaces between chains.
- A–B · 3624 Ų buried · 48 hydrogen bonds · protein-protein
- A–C · 3394 Ų buried · 44 hydrogen bonds · protein-protein
- B–C · 3120 Ų buried · 35 hydrogen bonds · protein-protein
- B–D · 972 Ų buried · 11 hydrogen bonds · protein-protein
- A–E · 898 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 6ZOH · 3-Formylrifamycin SV binding to the access pocket of AcrB-G619P_G621P L and T protomers · 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 6ZOH · PDBe 6ZOH · UniProt P31224
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