MolNFT v1 · #104771 · protein
The crystal structure of the pyocin S2 nuclease domain, immunity protein complex at 1.8 ångströms
4QKO · Pyocin-S2 immunity protein: “The crystal structure of the pyocin S2 nuclease domain, immunity protein complex at 1.8 ångströms”. X-ray diffraction, 2 ligands (MG, BR), 11 pockets (best druggability 0.76). MolNFT v1 #104771 on…
- 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
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