Research workbench
Cryo-EM structure of escherichia COLI acrbz and darpin in saposin a- nanodisc
Analyse Cryo-EM structure of escherichia COLI acrbz 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
- 6SGS
- Type
- protein
- Length
- 3,528 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Multidrug efflux pump subunit acrb; Darpin; Multidrug efflux pump accessory protein acrz
- UniProt
- P31224, I6DQK7
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 6 distinct chains · 54% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Multidrug efflux pump subunit acrb | protein | 1044 | 51% helix, 18% strand | P31224 |
| B, C | Multidrug efflux pump subunit acrb | protein | 1033 | 53% 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 | 92% helix, 0% strand | I6DQK7 |
| G | Multidrug efflux pump accessory protein acrz | protein | 36 | 92% helix, 0% strand | I6DQK7 |
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 | 837 | 0.88 | 0.90 | 111 | empty |
| 2 | 1177 | 0.86 | 0.87 | 130 | empty |
| 3 | 1132 | 0.83 | 0.84 | 94 | empty |
| 4 | 575 | 0.83 | 0.88 | 49 | empty |
| 5 | 289 | 0.80 | 0.91 | 37 | empty |
Interfaces
10 interfaces between chains.
- A–B · 3584 Ų buried · 30 hydrogen bonds · protein-protein
- A–C · 3421 Ų buried · 30 hydrogen bonds · protein-protein
- B–C · 3063 Ų buried · 26 hydrogen bonds · protein-protein
- C–F · 1329 Ų buried · 6 hydrogen bonds · protein-protein
- B–H · 1294 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6SGS · Cryo-EM structure of Escherichia coli AcrBZ and DARPin in Saposin A-nanodisc · the same entry in another collection · chain H against H, 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
- Every structure of UniProt I6DQK7
- Elsewhere: RCSB PDB 6SGS · PDBe 6SGS · UniProt P31224 · UniProt I6DQK7
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