Research workbench
Crystal structure of bacteriophage T4 spackle and lysozyme in orthorhombic form
Analyse Crystal structure of bacteriophage T4 spackle and lysozyme in orthorhombic form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XC1
- Type
- protein
- Length
- 243 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysozyme; Protein spackle
- EC
- 3.2.1.17
- UniProt
- P16009, P39230
- Pockets
- 3 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 68% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysozyme (EC 3.2.1.17) | protein | 167 | 64% helix, 8% strand | P16009 |
| C | Protein spackle | protein | 76 | 78% helix, 3% strand | P39230 |
Ligands and binding sites
- IPA · Isopropyl alcohol · additive · 3 copies · chains A, C
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 455 | 0.67 | 0.79 | 52 | IPA |
| 2 | 73 | 0.39 | 0.78 | 14 | empty |
| 3 | 57 | 0.31 | 0.76 | 14 | empty |
Interfaces
1 interface between chains.
- A–C · 1008 Ų buried · 30 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6XC1 · Crystal structure of bacteriophage T4 spackle and lysozyme in orthorhombic form · 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 6XC1 · PDBe 6XC1 · UniProt P16009 · UniProt P39230
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