Research workbench
Crystal structure of bacteriophage T4 spackle and lysozyme in monoclinic form
Analyse Crystal structure of bacteriophage T4 spackle and lysozyme in monoclinic form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XC0
- Type
- protein
- Length
- 485 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysozyme; Protein spackle
- EC
- 3.2.1.17
- UniProt
- P16009, P39230
- Ligands
- CL
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 69% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Lysozyme (EC 3.2.1.17) | protein | 167 | 63% helix, 8% strand | P16009 |
| C | Protein spackle | protein | 76 | 78% helix, 3% strand | P39230 |
| D | Protein spackle | protein | 75 | 75% helix, 3% strand | P39230 |
Ligands and binding sites
- CL · Chloride ion · ion · 3 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, C, B, D
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 3 copies · chains A, B
- SIN · Succinic acid · additive · chains A
- FMT · Formic acid · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1117 | 0.76 | 0.79 | 84 | EPE, CL |
| 2 | 414 | 0.68 | 0.81 | 49 | EPE |
| 3 | 79 | 0.42 | 0.79 | 14 | empty |
| 4 | 84 | 0.41 | 0.78 | 14 | empty |
| 5 | 71 | 0.31 | 0.75 | 18 | empty |
Interfaces
3 interfaces between chains.
- B–D · 1028 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 1002 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 465 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6XC0 · Crystal structure of bacteriophage T4 spackle and lysozyme in monoclinic 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 6XC0 · PDBe 6XC0 · UniProt P16009 · UniProt P39230
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