MolNFT v1 · #112989 · protein
Structure of bacteriophage SPP1 head-to-tail interface without DNA and tape measure protein
5A21 · Portal protein: “Structure of bacteriophage SPP1 head-to-tail interface without DNA and tape measure protein”. Electron microscopy, 20 pockets (best druggability 0.86). MolNFT v1 #112989 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5A21
- 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 · 31% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Portal protein | protein | 439 | 42% helix, 8% strand | P54309 |
| C, D | 15 protein | protein | 99 | 53% helix, 3% strand | Q38584 |
| E, F | Head completion protein GP16 | protein | 109 | 0% helix, 20% strand | O48446 |
| G | Tail-to-head joining protein GP17 | protein | 133 | 28% helix, 16% strand | O48448 |
| H | Major tail protein 17.1 | protein | 161 | 12% helix, 7% strand | O48449 |
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 984 | 0.86 | 0.87 | 95 | empty |
| 2 | 887 | 0.86 | 0.88 | 103 | empty |
| 3 | 855 | 0.85 | 0.87 | 105 | empty |
| 4 | 846 | 0.78 | 0.81 | 67 | empty |
| 5 | 248 | 0.75 | 0.88 | 35 | empty |
Interfaces
14 interfaces between chains.
- A–B · 4581 Ų buried · 116 hydrogen bonds · protein-protein
- E–F · 1667 Ų buried · 44 hydrogen bonds · protein-protein
- C–D · 1523 Ų buried · 41 hydrogen bonds · protein-protein
- G–H · 1153 Ų buried · 79 hydrogen bonds · protein-protein
- C–E · 793 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 5A21 · Structure of bacteriophage SPP1 head-to-tail interface without DNA and tape measure… · the same entry in another collection · chain G against G, 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 5A21 · PDBe 5A21 · UniProt P54309 · UniProt Q38584 · UniProt O48446 · UniProt O48448 · UniProt O48449
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