Research workbench
Avd molecule from bordetella bacteriophage dgr
Analyse Avd molecule from bordetella bacteriophage dgr in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DWL
- Type
- protein
- Length
- 545 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- BBP7
- UniProt
- Q775D7
- Ligands
- PO4
- Pockets
- 5 · best druggability 0.61
Structure
x-ray diffraction · 5 distinct chains · 84% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | BBP7 | protein | 109 | 84% helix, 0% strand | Q775D7 |
| B | BBP7 | protein | 110 | 85% helix, 0% strand | Q775D7 |
| E | BBP7 | protein | 109 | 83% helix, 0% strand | Q775D7 |
| C | BBP7 | protein | 110 | 84% helix, 0% strand | Q775D7 |
| D | BBP7 | protein | 107 | 84% helix, 0% strand | Q775D7 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · chains A, B, E, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 516 | 0.61 | 0.74 | 62 | empty |
| 2 | 306 | 0.50 | 0.73 | 46 | PO4 |
| 3 | 76 | 0.32 | 0.74 | 15 | empty |
| 4 | 61 | 0.31 | 0.75 | 14 | empty |
| 5 | 61 | 0.30 | 0.74 | 11 | empty |
Interfaces
5 interfaces between chains.
- A–B · 771 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 759 Ų buried · 7 hydrogen bonds · protein-protein
- A–E · 721 Ų buried · 6 hydrogen bonds · protein-protein
- E–D · 717 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 686 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 19 modified (engineered).
Compared structures
- 4DWL · Avd molecule from Bordetella bacteriophage DGR · the same entry in another collection · chain D against D, 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 Q775D7
- Elsewhere: RCSB PDB 4DWL · PDBe 4DWL · UniProt Q775D7
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