MolNFT v1 · #134845 · protein + DNA
RESTRICTION/MODIFICATION system-type II R.SWAI cleaved DNA complex
5TH3 · R-swai protein: “RESTRICTION/MODIFICATION system-type II R.SWAI cleaved DNA complex”. X-ray diffraction, 1 ligand (MG), 16 pockets (best druggability 0.76). MolNFT v1 #134845 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5TH3
- Type
- protein + DNA
- Length
- 1,008 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- R-swai protein; DNA (cleaved 25-mer, portion 1); DNA (cleaved 25-mer, portion 2); DNA…
- Ligands
- MG
- Pockets
- 16 · best druggability 0.76
Structure
x-ray diffraction · 8 distinct chains · 42% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | R-swai protein | protein | 226 | 42% helix, 26% strand | — |
| H | DNA (cleaved 25-mer, portion 1) | dna | 12 | — | — |
| h, j | DNA (cleaved 25-mer, portion 2) | dna | 13 | — | — |
| I | DNA (cleaved 26-mer, portion 1) | dna | 14 | — | — |
| i | DNA (cleaved 26-mer, portion 2) | dna | 12 | — | — |
| J | DNA (cleaved 25-mer, portion 1) | dna | 14 | — | — |
| K | DNA (cleaved 26-mer, portion 1) | dna | 13 | — | — |
| k | DNA (cleaved 26-mer, portion 2) | dna | 13 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 6 copies · chains A, h, H, B, i, C, j, D, k, K
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, D, h, I
- ACT · Acetate ion · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 893 | 0.76 | 0.80 | 82 | empty |
| 2 | 1143 | 0.75 | 0.78 | 94 | empty |
| 3 | 69 | 0.72 | 0.98 | 26 | empty |
| 4 | 357 | 0.66 | 0.81 | 41 | EDO |
| 5 | 449 | 0.66 | 0.79 | 50 | empty |
Interfaces
30 interfaces between chains.
- C–D · 2361 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 2306 Ų buried · 21 hydrogen bonds · protein-protein
- D–k · 633 Ų buried · 19 hydrogen bonds · protein-nucleic
- C–j · 619 Ų buried · 20 hydrogen bonds · protein-nucleic
- A–h · 618 Ų buried · 20 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 20 modified (engineered).
Compared structures
- 5TH3 · Restriction/modification system-Type II R.SwaI cleaved DNA complex · 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 5TH3 · PDBe 5TH3
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