MolNFT v1 · #117690 · protein
The host-recognition device of staphylococcus aureus phage PHI11
5EFV · Phi eta orf 56-like protein: “The host-recognition device of staphylococcus aureus phage PHI11”. X-ray diffraction, 1 ligand (FE), 20 pockets (best druggability 0.89). MolNFT v1 #117690 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5EFV
- Type
- protein
- Length
- 1,896 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phi eta orf 56-like protein
- UniProt
- Q8SDT4
- Ligands
- FE
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 3 distinct chains · 22% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phi eta orf 56-like protein | protein | 631 | 21% helix, 34% strand | Q8SDT4 |
| B | Phi eta orf 56-like protein | protein | 635 | 22% helix, 34% strand | Q8SDT4 |
| C | Phi eta orf 56-like protein | protein | 630 | 23% helix, 34% strand | Q8SDT4 |
Ligands and binding sites
- FE · Fe (III) ion · metal · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 923 | 0.89 | 0.91 | 82 | empty |
| 2 | 995 | 0.89 | 0.90 | 121 | empty |
| 3 | 488 | 0.88 | 0.95 | 51 | empty |
| 4 | 751 | 0.84 | 0.87 | 95 | empty |
| 5 | 108 | 0.79 | 0.98 | 16 | empty |
Interfaces
3 interfaces between chains.
- B–C · 6219 Ų buried · 95 hydrogen bonds · protein-protein
- A–B · 6163 Ų buried · 94 hydrogen bonds · protein-protein
- A–C · 6077 Ų buried · 84 hydrogen bonds · protein-protein
Compared structures
- 5EFV · The host-recognition device of Staphylococcus aureus phage Phi11 · 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 Q8SDT4
- Elsewhere: RCSB PDB 5EFV · PDBe 5EFV · UniProt Q8SDT4
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