Research workbench
A polyamorous repressor: deciphering the evolutionary strategy used by the phage-inducible chromosomal islands to spread in nature.
Analyse A polyamorous repressor: deciphering the evolutionary strategy used by the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6H4C
- Type
- protein
- Length
- 1,199 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dutpase; ORF20
- UniProt
- Q8SDV3, Q9F0J8
- Ligands
- NI, MG
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 7 distinct chains · 42% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Dutpase | protein | 153 | 4% helix, 48% strand | Q8SDV3 |
| B | ORF20 | protein | 147 | 72% helix, 1% strand | Q9F0J8 |
| D | ORF20 | protein | 148 | 70% helix, 1% strand | Q9F0J8 |
| E | Dutpase | protein | 154 | 4% helix, 47% strand | Q8SDV3 |
| F | ORF20 | protein | 144 | 73% helix, 0% strand | Q9F0J8 |
| G | Dutpase | protein | 155 | 4% helix, 41% strand | Q8SDV3 |
| H | ORF20 | protein | 145 | 71% helix, 0% strand | Q9F0J8 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · 5 copies · chains A, F, B, C, E, H
- MG · Magnesium ion · metal · 2 copies · chains A, C, E, G
- PEG · Di(hydroxyethyl)ether · additive · 7 copies · chains C, E, D, A, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 485 | 0.87 | 0.94 | 66 | PEG |
| 2 | 160 | 0.80 | 0.96 | 42 | empty |
| 3 | 145 | 0.80 | 0.97 | 38 | empty |
| 4 | 121 | 0.79 | 0.98 | 25 | empty |
| 5 | 949 | 0.75 | 0.78 | 97 | NI |
Interfaces
13 interfaces between chains.
- A–C · 1584 Ų buried · 20 hydrogen bonds · protein-protein
- C–E · 1569 Ų buried · 22 hydrogen bonds · protein-protein
- A–E · 1561 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 792 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 748 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 6H4C · A polyamorous repressor: deciphering the evolutionary strategy used by the… · 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 Q8SDV3
- Every structure of UniProt Q9F0J8
- Elsewhere: RCSB PDB 6H4C · PDBe 6H4C · UniProt Q8SDV3 · UniProt Q9F0J8
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