MolNFT v2 · #148004 · protein
Crystal structure of the Acinetobacter phage vB_ApiP_P1 tailspike protein
6E1R: “Crystal structure of the Acinetobacter phage vB_ApiP_P1 tailspike protein”. X-ray diffraction at 2.693, 2 ligands (NA, CL), 20 pockets (best druggability 0.89). MolNFT v2 #148004 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 6E1R
- Type
- protein
- Length
- 3,263 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.693
- Source
- Acinetobacter phage vB_ApiP_P1
- Molecule
- Tailspike protein
- UniProt
- A0A221SBY4
- Ligands
- NA, CL
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · resolution 2.693 · 2 distinct chains · 6% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, E, F | Tailspike protein | protein | 544 | 6% helix, 48% strand | A0A221SBY4 |
| B | Tailspike protein | protein | 543 | 6% helix, 49% strand | A0A221SBY4 |
Ligands and binding sites
- NA · Sodium ion · metal · 3 copies · chains B, C, A, D, E, F
- CL · Chloride ion · ion · 3 copies · chains A, B, C, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 938 | 0.89 | 0.91 | 128 | empty |
| 2 | 991 | 0.88 | 0.89 | 131 | empty |
| 3 | 97 | 0.78 | 0.98 | 28 | empty |
| 4 | 81 | 0.77 | 0.99 | 22 | CL |
| 5 | 86 | 0.77 | 0.99 | 27 | empty |
Interfaces
8 interfaces between chains.
- D–F · 4161 Ų buried · 73 hydrogen bonds · protein-protein
- D–E · 4137 Ų buried · 83 hydrogen bonds · protein-protein
- B–C · 4127 Ų buried · 79 hydrogen bonds · protein-protein
- E–F · 4118 Ų buried · 75 hydrogen bonds · protein-protein
- A–C · 4064 Ų buried · 82 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 66 modified (engineered).
Compared structures
- 6E1R · Crystal structure of the acinetobacter phage VB_APIP_P1 tailspike protein · the same entry in another collection · chain A against A, 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 A0A221SBY4
- Elsewhere: RCSB PDB 6E1R · PDBe 6E1R · UniProt A0A221SBY4
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