Research workbench
Sequential reorganization of beta-sheet topology by insertion of a single strand
Analyse Sequential reorganization of beta-sheet topology by insertion of a single strand in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3JR6
- Type
- protein
- Length
- 654 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysozyme
- EC
- 3.2.1.17
- UniProt
- P00720
- Ligands
- SO4
- Pockets
- 5 · best druggability 0.65
Structure
x-ray diffraction · 4 distinct chains · 63% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysozyme (EC 3.2.1.17) | protein | 170 | 61% helix, 9% strand | P00720 |
| B | Lysozyme (EC 3.2.1.17) | protein | 156 | 66% helix, 4% strand | P00720 |
| C | Lysozyme (EC 3.2.1.17) | protein | 159 | 61% helix, 4% strand | P00720 |
| D | Lysozyme (EC 3.2.1.17) | protein | 169 | 63% helix, 11% strand | P00720 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 8 copies · chains A, B, C, D
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 | 594 | 0.65 | 0.75 | 51 | SO4 |
| 2 | 309 | 0.57 | 0.76 | 29 | empty |
| 3 | 166 | 0.49 | 0.77 | 28 | empty |
| 4 | 210 | 0.48 | 0.75 | 24 | empty |
| 5 | 65 | 0.29 | 0.74 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1194 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 165 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 44 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3JR6 · Sequential reorganization of beta-sheet topology by insertion of a single strand · 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 3JR6 · PDBe 3JR6 · UniProt P00720
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