Research workbench
Structure of the two C-terminal domains of bacteriophage K GP144
Analyse Structure of the two C-terminal domains of bacteriophage K GP144 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5M9F
- Type
- protein
- Length
- 634 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ORF68
- UniProt
- Q6Y7P9
- Ligands
- NA
- Pockets
- 8 · best druggability 0.89
Structure
x-ray diffraction · 2 distinct chains · 9% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | ORF68 | protein | 212 | 8% helix, 53% strand | Q6Y7P9 |
| C | ORF68 | protein | 210 | 10% helix, 54% strand | Q6Y7P9 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 434 | 0.89 | 0.97 | 55 | ACT |
| 2 | 220 | 0.63 | 0.83 | 35 | empty |
| 3 | 86 | 0.38 | 0.77 | 22 | empty |
| 4 | 90 | 0.38 | 0.76 | 22 | empty |
| 5 | 50 | 0.34 | 0.79 | 13 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1667 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 1646 Ų buried · 27 hydrogen bonds · protein-protein
- B–C · 1539 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 5M9F · Structure of the two C-terminal domains of bacteriophage K gp144 · 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 Q6Y7P9
- Elsewhere: RCSB PDB 5M9F · PDBe 5M9F · UniProt Q6Y7P9
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