Research workbench
Structure of the carboxy-terminal domain of the bacteriophage T5 L- shaped tail fiber without its intra-molecular chaperone domain
Analyse Structure of the carboxy-terminal domain of the bacteriophage T5 L- shaped tail… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4UW7
- Type
- protein
- Length
- 825 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-shaped tail fiber protein
- UniProt
- Q5DMH0
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-shaped tail fiber protein | protein | 274 | 7% helix, 41% strand | Q5DMH0 |
| B | L-shaped tail fiber protein | protein | 275 | 7% helix, 41% strand | Q5DMH0 |
| C | L-shaped tail fiber protein | protein | 276 | 7% helix, 42% strand | Q5DMH0 |
Ligands and binding sites
- GOL · Glycerol · additive · 3 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 55 | 0.72 | 0.98 | 22 | empty |
| 2 | 79 | 0.32 | 0.74 | 16 | empty |
| 3 | 78 | 0.31 | 0.73 | 16 | empty |
| 4 | 69 | 0.31 | 0.75 | 19 | empty |
| 5 | 59 | 0.26 | 0.73 | 18 | empty |
Interfaces
3 interfaces between chains.
- B–C · 6198 Ų buried · 121 hydrogen bonds · protein-protein
- A–B · 6177 Ų buried · 120 hydrogen bonds · protein-protein
- A–C · 6106 Ų buried · 116 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 modified (engineered).
Compared structures
- 4UW7 · Structure of the carboxy-terminal domain of the bacteriophage T5 L- shaped tail fiber… · 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 Q5DMH0
- Elsewhere: RCSB PDB 4UW7 · PDBe 4UW7 · UniProt Q5DMH0
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