MolNFT v1 · #159011 · protein + DNA
Structure of a DNA-bound dimer extracted from filamentous sgrai endonuclease in its activated form
6OBJ · Sgrair restriction enzyme: “Structure of a DNA-bound dimer extracted from filamentous sgrai endonuclease in its activated form”. Electron microscopy, 1 ligand (MG), 8 pockets (best druggability 0.71). MolNFT v1 #159011 on GenesisL1…
- PDB
- 6OBJ
- Type
- protein + DNA
- Length
- 728 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sgrair restriction enzyme; DNA (26-mer)
- EC
- 3.1.21.-
- UniProt
- Q9F6L0
- Ligands
- MG
- Pockets
- 8 · best druggability 0.71
Structure
electron microscopy · 2 distinct chains · 39% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Sgrair restriction enzyme (EC 3.1.21.-) | protein | 338 | 39% helix, 11% strand | Q9F6L0 |
| C, D | DNA (26-mer) | dna | 26 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 282 | 0.71 | 0.86 | 35 | empty |
| 2 | 310 | 0.71 | 0.85 | 39 | empty |
| 3 | 365 | 0.58 | 0.76 | 35 | empty |
| 4 | 304 | 0.57 | 0.77 | 33 | empty |
| 5 | 164 | 0.43 | 0.75 | 20 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1622 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 1256 Ų buried · 117 hydrogen bonds · nucleic-nucleic
- C–B · 968 Ų buried · 16 hydrogen bonds · protein-nucleic
- A–D · 968 Ų buried · 17 hydrogen bonds · protein-nucleic
- B–D · 798 Ų buried · 16 hydrogen bonds · protein-nucleic
Compared structures
- 6OBJ · Structure of a DNA-bound dimer extracted from filamentous SgrAI endonuclease in its… · 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 Q9F6L0
- Elsewhere: RCSB PDB 6OBJ · PDBe 6OBJ · UniProt Q9F6L0
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