Research workbench
Structure of bacteriophage SPP1 head-to-tail interface filled with DNA and tape measure protein
Analyse Structure of bacteriophage SPP1 head-to-tail interface filled with DNA and tape… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5A20
- Type
- protein
- Length
- 1,588 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Portal protein; 15 protein; Head completion protein GP16; Tail-to-head joining protein…
- UniProt
- P54309, Q38584, O48446, O48448, O48449
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 5 distinct chains · 33% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Portal protein | protein | 439 | 45% helix, 5% strand | P54309 |
| C, D | 15 protein | protein | 99 | 53% helix, 2% strand | Q38584 |
| E, F | Head completion protein GP16 | protein | 109 | 4% helix, 20% strand | O48446 |
| G | Tail-to-head joining protein GP17 | protein | 133 | 28% helix, 17% strand | O48448 |
| H | Major tail protein GP17.1 | protein | 161 | 16% helix, 11% strand | O48449 |
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 960 | 0.86 | 0.87 | 117 | empty |
| 2 | 884 | 0.84 | 0.86 | 85 | empty |
| 3 | 1061 | 0.82 | 0.83 | 73 | empty |
| 4 | 1018 | 0.79 | 0.80 | 92 | empty |
| 5 | 792 | 0.76 | 0.80 | 82 | empty |
Interfaces
14 interfaces between chains.
- A–B · 4451 Ų buried · 66 hydrogen bonds · protein-protein
- E–F · 1622 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 1414 Ų buried · 16 hydrogen bonds · protein-protein
- G–H · 1093 Ų buried · 54 hydrogen bonds · protein-protein
- F–G · 802 Ų buried · 44 hydrogen bonds · protein-protein
Compared structures
- 5A20 · Structure of bacteriophage SPP1 head-to-tail interface filled with DNA and tape measure… · 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 P54309
- Every structure of UniProt Q38584
- Every structure of UniProt O48446
- Every structure of UniProt O48448
- Every structure of UniProt O48449
- Elsewhere: RCSB PDB 5A20 · PDBe 5A20 · UniProt P54309 · UniProt Q38584 · UniProt O48446 · UniProt O48448 · UniProt O48449
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