MolNFT v1 · #175328 · protein
T4 phage spackle protein GP61.3 complex with lysozyme domain of GP5 tail lysozyme
7CN7 · Baseplate central spike complex protein GP5: “T4 phage spackle protein GP61.3 complex with lysozyme domain of GP5 tail lysozyme”. X-ray diffraction, 3 ligands (1PG, NA, CL), 2 pockets (best druggability 0.67). MolNFT v1 #175328 on…
- 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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