Research workbench
Designed ankyrin repeat protein (darpin) binders to acrb: plasticity of the interface
Analyse Designed ankyrin repeat protein (darpin) binders to acrb: plasticity of the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NOG
- Type
- protein
- Length
- 3,385 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acriflavine resistance protein B; Designed ankyrin repeat protein
- UniProt
- P31224
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 5 distinct chains · 48% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acriflavine resistance protein B | protein | 1012 | 48% helix, 18% strand | P31224 |
| B | Acriflavine resistance protein B | protein | 1028 | 49% helix, 18% strand | P31224 |
| C | Acriflavine resistance protein B | protein | 1040 | 49% helix, 16% strand | P31224 |
| D | Designed ankyrin repeat protein | protein | 154 | 54% helix, 0% strand | — |
| E | Designed ankyrin repeat protein | protein | 151 | 40% helix, 1% 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 | 1128 | 0.87 | 0.88 | 135 | empty |
| 2 | 799 | 0.86 | 0.89 | 91 | empty |
| 3 | 458 | 0.84 | 0.91 | 87 | empty |
| 4 | 577 | 0.81 | 0.86 | 87 | empty |
| 5 | 243 | 0.76 | 0.90 | 39 | empty |
Interfaces
7 interfaces between chains.
- A–B · 3309 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 3136 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 2788 Ų buried · 29 hydrogen bonds · protein-protein
- B–D · 969 Ų buried · 12 hydrogen bonds · protein-protein
- A–E · 546 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified (formylation).
Compared structures
- 3NOG · Designed ankyrin repeat protein (DARPin) Binders to AcrB: Plasticity of the Interface · 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 0.97
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 3NOG · PDBe 3NOG · UniProt P31224
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