Research workbench
Structure of the tripod (bppuct-a-L) from the baseplate of bacteriophage TUC2009
Analyse Structure of the tripod (bppuct-a-L) from the baseplate of bacteriophage TUC2009 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5E7T
- Type
- protein
- Length
- 1,053 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Minor structural protein 4; Minor structural protein 5; Major structural protein 1
- UniProt
- Q9AYV5, Q9AYV4, Q38610
- Ligands
- CA, SO4
- Pockets
- 7 · best druggability 0.75
Structure
x-ray diffraction · 5 distinct chains · 8% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Minor structural protein 4 | protein | 129 | 2% helix, 47% strand | Q9AYV5 |
| B | Minor structural protein 5 | protein | 286 | 6% helix, 45% strand | Q9AYV4 |
| G, I | Major structural protein 1 | protein | 172 | 12% helix, 47% strand | Q38610 |
| H | Major structural protein 1 | protein | 173 | 12% helix, 47% strand | Q38610 |
| L | Major structural protein 1 | protein | 121 | 7% helix, 42% strand | Q38610 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 59 | 0.75 | 1.00 | 18 | empty |
| 2 | 396 | 0.61 | 0.76 | 45 | empty |
| 3 | 153 | 0.60 | 0.84 | 28 | CA |
| 4 | 278 | 0.49 | 0.73 | 34 | empty |
| 5 | 106 | 0.46 | 0.79 | 16 | empty |
Interfaces
8 interfaces between chains.
- G–I · 2896 Ų buried · 58 hydrogen bonds · protein-protein
- G–H · 2891 Ų buried · 52 hydrogen bonds · protein-protein
- H–I · 2807 Ų buried · 49 hydrogen bonds · protein-protein
- A–B · 1090 Ų buried · 17 hydrogen bonds · protein-protein
- B–L · 704 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 5E7T · Structure of the tripod (BppUct-A-L) from the baseplate of bacteriophage Tuc2009 · 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 Q9AYV5
- Every structure of UniProt Q9AYV4
- Every structure of UniProt Q38610
- Elsewhere: RCSB PDB 5E7T · PDBe 5E7T · UniProt Q9AYV5 · UniProt Q9AYV4 · UniProt Q38610
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