MolNFT v1 · #127963 · protein
Crystal structure of acrbz in complex with antibiotic puromycin
5NC5 · Multidrug efflux pump subunit acrb: “Crystal structure of acrbz in complex with antibiotic puromycin”. X-ray diffraction, 3 ligands (D10, D12, PUY), 20 pockets (best druggability 0.87). MolNFT v1 #127963 on GenesisL1: 3D structure…
- PDB
- 5NC5
- Type
- protein
- Length
- 3,528 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Multidrug efflux pump subunit acrb; Darpin; Multidrug efflux pump accessory protein acrz
- UniProt
- P31224, P0AAX1
- Ligands
- D10, D12, PUY
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 6 distinct chains · 55% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Multidrug efflux pump subunit acrb | protein | 1044 | 54% helix, 19% strand | P31224 |
| B, C | Multidrug efflux pump subunit acrb | protein | 1033 | 55% helix, 19% strand | P31224 |
| D | Darpin | protein | 156 | 53% helix, 0% strand | — |
| E | Darpin | protein | 152 | 53% helix, 0% strand | — |
| F, H | Multidrug efflux pump accessory protein acrz | protein | 37 | 89% helix, 0% strand | P0AAX1 |
| G | Multidrug efflux pump accessory protein acrz | protein | 36 | 92% helix, 0% strand | P0AAX1 |
Ligands and binding sites
- D10 · Decane · ligand · 26 copies · chains A, C, B
- D12 · Dodecane · ligand · 8 copies · chains A, B, C
- PUY · Puromycin · ligand · chains B
- DD9 · nonane · additive · 14 copies · chains A, B, C
- LMT · Dodecyl-beta-D-maltoside · additive · 3 copies · chains A, C, B
- HEX · Hexane · additive · 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 | 750 | 0.87 | 0.91 | 93 | empty |
| 2 | 677 | 0.86 | 0.90 | 86 | empty |
| 3 | 706 | 0.85 | 0.89 | 102 | empty |
| 4 | 590 | 0.81 | 0.87 | 50 | empty |
| 5 | 587 | 0.81 | 0.86 | 36 | empty |
Interfaces
10 interfaces between chains.
- A–B · 3546 Ų buried · 40 hydrogen bonds · protein-protein
- A–C · 3370 Ų buried · 34 hydrogen bonds · protein-protein
- B–C · 2953 Ų buried · 39 hydrogen bonds · protein-protein
- C–F · 1243 Ų buried · 6 hydrogen bonds · protein-protein
- B–H · 1193 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5NC5 · Crystal structure of AcrBZ in complex with antibiotic puromycin · the same entry in another collection · chain B against B, 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
- P0AAX1 · AlphaFold monomer V2.0 prediction for multidrug efflux pump accessory protein acrz… · a predicted model of the same protein · chain H against A, TM-score 0.84
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
- Every structure of UniProt P0AAX1
- Elsewhere: RCSB PDB 5NC5 · PDBe 5NC5 · UniProt P31224 · UniProt P0AAX1
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