Research workbench
RESTRICTION/MODIFICATION system-type II R-swai complexed with partially cleaved DNA
Analyse RESTRICTION/MODIFICATION system-type II R-swai complexed with partially cleaved… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TGX
- Type
- protein + DNA
- Length
- 1,005 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- R-swai protein; DNA (26-mer)
- Ligands
- CA
- Pockets
- 17 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | R-swai protein | protein | 225 | 42% helix, 25% strand | — |
| H | DNA (26-mer) | dna | 26 | — | — |
| I, K | DNA (26-mer) | dna | 26 | — | — |
| J | DNA (26-mer) | dna | 27 | — | — |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, H, B, I, C, J, D, K
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, D, I, J, H
- ACT · Acetate ion · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 407 | 0.71 | 0.82 | 42 | EDO |
| 2 | 157 | 0.71 | 0.90 | 22 | empty |
| 3 | 170 | 0.71 | 0.89 | 23 | empty |
| 4 | 425 | 0.70 | 0.82 | 45 | empty |
| 5 | 635 | 0.68 | 0.77 | 50 | empty |
Interfaces
14 interfaces between chains.
- C–D · 2336 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 2325 Ų buried · 20 hydrogen bonds · protein-protein
- J–K · 1278 Ų buried · 104 hydrogen bonds · nucleic-nucleic
- H–I · 1236 Ų buried · 100 hydrogen bonds · nucleic-nucleic
- D–K · 981 Ų buried · 26 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 16 modified (engineered).
Compared structures
- 5TGX · Restriction/modification system-Type II R-SwaI complexed with partially cleaved DNA · 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
- Elsewhere: RCSB PDB 5TGX · PDBe 5TGX
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