Research workbench
The crystal structure of the pyocin S2 nuclease domain, immunity protein complex at 1.8 ångströms
Analyse The crystal structure of the pyocin S2 nuclease domain, immunity protein… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4QKO
- Type
- protein
- Length
- 873 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyocin-S2 immunity protein; Pyocin-S2
- EC
- 3.1.-.-
- UniProt
- Q06579, Q06584
- Ligands
- MG, BR
- Pockets
- 11 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 47% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Pyocin-S2 immunity protein | protein | 87 | 55% helix, 2% strand | Q06579 |
| B, F, H | Pyocin-S2 (EC 3.1.-.-) | protein | 131 | 42% helix, 17% strand | Q06584 |
| D | Pyocin-S2 (EC 3.1.-.-) | protein | 133 | 42% helix, 17% strand | Q06584 |
| G | Pyocin-S2 immunity protein | protein | 86 | 56% helix, 2% strand | Q06579 |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains B, D, F, H
- BR · Bromide ion · ion · 35 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1060 | 0.76 | 0.78 | 108 | BR, MG |
| 2 | 436 | 0.60 | 0.75 | 64 | BR |
| 3 | 51 | 0.53 | 0.89 | 17 | empty |
| 4 | 96 | 0.51 | 0.82 | 20 | BR |
| 5 | 104 | 0.48 | 0.80 | 23 | BR |
Interfaces
14 interfaces between chains.
- C–D · 855 Ų buried · 22 hydrogen bonds · protein-protein
- E–F · 853 Ų buried · 21 hydrogen bonds · protein-protein
- G–H · 844 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 791 Ų buried · 19 hydrogen bonds · protein-protein
- B–E · 166 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4QKO · The Crystal Structure of the Pyocin S2 Nuclease Domain, Immunity Protein Complex at 1.8… · the same entry in another collection · chain H against H, TM-score 1.00
- Q06579 · AlphaFold monomer V2.0 prediction for pyocin-S2 immunity protein (Q06579) · a predicted model of the same protein · chain A against A, TM-score 0.98
- Q06584 · AlphaFold monomer V2.0 prediction for pyocin-S2 (Q06584) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 Q06579
- Every structure of UniProt Q06584
- Elsewhere: RCSB PDB 4QKO · PDBe 4QKO · UniProt Q06579 · UniProt Q06584
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.