Research workbench
Structure of the bacteriophage T5 distal tail protein PB9 co- crystallized with 10MM tb-XO4
Analyse Structure of the bacteriophage T5 distal tail protein PB9 co- crystallized with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6F2M
- Type
- protein
- Length
- 727 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Distal tail protein
- UniProt
- Q6QGE8
- Ligands
- 7MT, TB, NA, CL
- Pockets
- 4 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 14% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Distal tail protein | protein | 185 | 14% helix, 36% strand | Q6QGE8 |
| B | Distal tail protein | protein | 172 | 15% helix, 38% strand | Q6QGE8 |
Ligands and binding sites
- 7MT · Tb-Xo4 · ligand · 3 copies · chains A, C, D
- TB · Terbium(iii) ion · metal · 2 copies · chains B, D
- NA · Sodium ion · metal · chains A
- CL · Chloride ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 423 | 0.65 | 0.79 | 50 | empty |
| 2 | 547 | 0.65 | 0.77 | 63 | empty |
| 3 | 122 | 0.38 | 0.74 | 20 | empty |
| 4 | 113 | 0.35 | 0.73 | 21 | empty |
Interfaces
4 interfaces between chains.
- B–D · 708 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 456 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 452 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 25 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6F2M · Structure of the bacteriophage T5 distal tail protein pb9 co-crystallized with 10mM Tb-Xo4 · 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 Q6QGE8
- Elsewhere: RCSB PDB 6F2M · PDBe 6F2M · UniProt Q6QGE8
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