Research workbench
Cryo-EM structure of escherichia COLI acrb and darpin in saposin a- nanodisc
Analyse Cryo-EM structure of escherichia COLI acrb and darpin in saposin a- nanodisc in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6SGU
- Type
- protein
- Length
- 3,407 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Multidrug efflux pump subunit acrb; Darpin
- UniProt
- P31224
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 3 distinct chains · 48% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Multidrug efflux pump subunit acrb | protein | 1033 | 48% helix, 18% strand | P31224 |
| D | Darpin | protein | 156 | 47% helix, 0% strand | — |
| E | Darpin | protein | 152 | 48% helix, 0% strand | — |
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 | 872 | 0.87 | 0.90 | 99 | empty |
| 2 | 1086 | 0.86 | 0.87 | 129 | empty |
| 3 | 816 | 0.86 | 0.88 | 82 | empty |
| 4 | 880 | 0.83 | 0.86 | 87 | empty |
| 5 | 400 | 0.81 | 0.89 | 65 | empty |
Interfaces
7 interfaces between chains.
- A–B · 3598 Ų buried · 35 hydrogen bonds · protein-protein
- A–C · 3406 Ų buried · 30 hydrogen bonds · protein-protein
- B–C · 3143 Ų buried · 38 hydrogen bonds · protein-protein
- B–D · 1004 Ų buried · 13 hydrogen bonds · protein-protein
- A–E · 828 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6SGU · Cryo-EM structure of Escherichia coli AcrB and DARPin in Saposin A-nanodisc · 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 6SGU · PDBe 6SGU · UniProt P31224
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