MolNFT v1 · #126842 · protein
Bacteriophage T5 distal tail protein PB9 co-crystallized with tb-XO4
5MF2: “Bacteriophage T5 distal tail protein PB9 co-crystallized with tb-XO4”. X-ray diffraction, 3 ligands (7MT, TB, CL), 6 pockets (best druggability 0.69). MolNFT v1 #126842 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5MF2
- Type
- protein
- Length
- 732 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Distal tail protein
- UniProt
- Q6QGE8
- Ligands
- 7MT, TB, CL
- Pockets
- 6 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 15% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Distal tail protein | protein | 185 | 14% helix, 34% strand | Q6QGE8 |
| B | Distal tail protein | protein | 173 | 15% helix, 36% strand | Q6QGE8 |
| C, D | Distal tail protein | protein | 187 | 16% helix, 37% strand | Q6QGE8 |
Ligands and binding sites
- 7MT · Tb-Xo4 · ligand · 3 copies · chains A, C, D
- TB · Terbium(iii) ion · metal · 12 copies · chains A, B, D
- CL · Chloride ion · ion · 4 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 682 | 0.69 | 0.77 | 67 | CL |
| 2 | 418 | 0.64 | 0.78 | 41 | CL |
| 3 | 132 | 0.40 | 0.74 | 20 | empty |
| 4 | 60 | 0.40 | 0.81 | 15 | empty |
| 5 | 148 | 0.38 | 0.73 | 20 | empty |
Interfaces
4 interfaces between chains.
- A–B · 715 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 453 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 453 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 73 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5MF2 · Bacteriophage T5 distal tail protein pb9 co-crystallized with 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 5MF2 · PDBe 5MF2 · UniProt Q6QGE8
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