Research workbench
T4 phage spackle protein GP61.3 complex with lysozyme domain of GP5 tail lysozyme
Analyse T4 phage spackle protein GP61.3 complex with lysozyme domain of GP5 tail… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7CN7
- Type
- protein
- Length
- 253 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Baseplate central spike complex protein GP5; Protein spackle
- EC
- 3.2.1.17
- UniProt
- P16009, P39230
- Ligands
- 1PG, NA, CL
- Pockets
- 2 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 65% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Baseplate central spike complex protein GP5 (EC 3.2.1.17) | protein | 178 | 60% helix, 7% strand | P16009 |
| C | Protein spackle | protein | 75 | 79% helix, 3% strand | P39230 |
Ligands and binding sites
- 1PG · 2-(2-{2-[2-(2-methoxy-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethanol · ligand · chains A
- NA · Sodium ion · metal · 3 copies · chains A, C
- CL · Chloride ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 429 | 0.67 | 0.79 | 47 | empty |
| 2 | 60 | 0.33 | 0.77 | 16 | empty |
Interfaces
1 interface between chains.
- A–C · 918 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 7CN7 · T4 phage spackle protein gp61.3 complex with lysozyme domain of gp5 tail lysozyme · 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 P16009
- Every structure of UniProt P39230
- Elsewhere: RCSB PDB 7CN7 · PDBe 7CN7 · UniProt P16009 · UniProt P39230
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