Research workbench
Zn-mediated hexamer of T4 lysozyme R76H/R80H by synthetic symmetrization
Analyse Zn-mediated hexamer of T4 lysozyme R76H/R80H by synthetic symmetrization in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3SBA
- Type
- protein
- Length
- 976 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysozyme
- EC
- 3.2.1.17
- UniProt
- P00720
- Ligands
- ZN, CL
- Pockets
- 9 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 62% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Lysozyme (EC 3.2.1.17) | protein | 162 | 63% helix, 9% strand | P00720 |
| B, D, E, F | Lysozyme (EC 3.2.1.17) | protein | 163 | 62% helix, 9% strand | P00720 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 295 | 0.84 | 0.95 | 38 | empty |
| 2 | 319 | 0.84 | 0.94 | 40 | empty |
| 3 | 264 | 0.84 | 0.95 | 38 | empty |
| 4 | 833 | 0.75 | 0.79 | 79 | empty |
| 5 | 1165 | 0.73 | 0.77 | 79 | empty |
Interfaces
6 interfaces between chains.
- B–C · 899 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 890 Ų buried · 16 hydrogen bonds · protein-protein
- C–E · 885 Ų buried · 12 hydrogen bonds · protein-protein
- D–F · 875 Ų buried · 13 hydrogen bonds · protein-protein
- A–F · 870 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 3SBA · Zn-mediated Hexamer of T4 Lysozyme R76H/R80H by Synthetic Symmetrization · 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 P00720
- Elsewhere: RCSB PDB 3SBA · PDBe 3SBA · UniProt P00720
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