MolNFT v1 · #128090 · protein
Multi-drug efflux; membrane transport; rnd superfamily; drug resistance
5NG5 · Multidrug efflux pump subunit acra: “Multi-drug efflux; membrane transport; rnd superfamily; drug resistance”. Electron microscopy, 1 ligand (5QF), 20 pockets (best druggability 0.89). MolNFT v1 #128090 on GenesisL1: 3D structure…
- PDB
- 5NG5
- Type
- protein
- Length
- 6,569 residues
- Chains
- 15
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Multidrug efflux pump subunit acra; Outer membrane protein tolc; Multidrug efflux pump…
- UniProt
- P0AE06, P02930, P31224, P0AAW9
- Ligands
- 5QF
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 5 distinct chains · 44% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E, D, G, H, A, B | Multidrug efflux pump subunit acra | protein | 340 | 21% helix, 22% strand | P0AE06 |
| F, I, C | Outer membrane protein tolc | protein | 428 | 64% helix, 17% strand | P02930 |
| K, L | Multidrug efflux pump subunit acrb | protein | 1037 | 42% helix, 15% strand | P31224 |
| M, N, O | Multidrug efflux pump accessory protein acrz | protein | 46 | 50% helix, 0% strand | P0AAW9 |
| J | Multidrug efflux pump subunit acrb | protein | 1033 | 45% helix, 13% strand | P31224 |
Ligands and binding sites
- 5QF · 6-[2-(3,4-dimethoxyphenyl)ethylsulfanyl]-8-[4-(2-methoxyethyl)piperazin-1-yl]-3,3-dimethyl-1,4-dihydropyrano[3,4-c]pyridine-5-carbonitrile · ligand · 3 copies · chains K, L, J
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 | 1169 | 0.89 | 0.91 | 150 | 5QF |
| 2 | 1094 | 0.89 | 0.91 | 135 | 5QF |
| 3 | 433 | 0.85 | 0.93 | 70 | empty |
| 4 | 331 | 0.82 | 0.92 | 53 | 5QF |
| 5 | 217 | 0.79 | 0.92 | 30 | empty |
Interfaces
36 interfaces between chains.
- L–J · 3816 Ų buried · 55 hydrogen bonds · protein-protein
- K–L · 3769 Ų buried · 49 hydrogen bonds · protein-protein
- K–J · 3652 Ų buried · 43 hydrogen bonds · protein-protein
- I–C · 2444 Ų buried · 49 hydrogen bonds · protein-protein
- F–C · 2431 Ų buried · 49 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 covalent (covalent ligand).
Compared structures
- 5NG5 · multi-drug efflux; membrane transport; RND superfamily; Drug resistance · the same entry in another collection · chain L against L, 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 P0AE06
- Every structure of UniProt P02930
- Every structure of UniProt P31224
- Every structure of UniProt P0AAW9
- Elsewhere: RCSB PDB 5NG5 · PDBe 5NG5 · UniProt P0AE06 · UniProt P02930 · UniProt P31224 · UniProt P0AAW9
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