MolNFT v1 · #187707 · protein + DNA
Activated sgrai endonuclease DNA-bound dimer with CA2+ and intact primary site DNA
7SS5 · Sgrair restriction enzyme: “Activated sgrai endonuclease DNA-bound dimer with CA2+ and intact primary site DNA”. Electron microscopy, 1 ligand (CA), 8 pockets (best druggability 0.75). MolNFT v1 #187707 on GenesisL1: 3D structure…
- PDB
- 7SS5
- Type
- protein + DNA
- Length
- 724 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sgrair restriction enzyme; DNA (5'- D(P*GP*GP*TP*CP*TP*TP*CP*AP*CP*AP*CP*CP*GP*GP*TP*GP*TP…
- UniProt
- Q9F6L0
- Ligands
- CA
- Pockets
- 8 · best druggability 0.75
Structure
electron microscopy · 2 distinct chains · 43% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Sgrair restriction enzyme | protein | 338 | 43% helix, 12% strand | Q9F6L0 |
| C, D | DNA (5'- D(P*GP*GP*TP*CP*TP*TP*CP*AP*CP*AP*CP*CP*GP*GP*TP*GP*TP*GP*AP*AP*GP*AP *CP*C)-3') | dna | 24 | — | — |
Ligands and binding sites
- CA · Calcium ion · metal · 6 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 637 | 0.75 | 0.81 | 66 | CA |
| 2 | 396 | 0.72 | 0.84 | 47 | CA |
| 3 | 339 | 0.58 | 0.77 | 41 | empty |
| 4 | 344 | 0.56 | 0.76 | 36 | empty |
| 5 | 164 | 0.51 | 0.79 | 28 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1552 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1101 Ų buried · 96 hydrogen bonds · nucleic-nucleic
- C–B · 931 Ų buried · 19 hydrogen bonds · protein-nucleic
- A–D · 928 Ų buried · 18 hydrogen bonds · protein-nucleic
- B–D · 789 Ų buried · 18 hydrogen bonds · protein-nucleic
Compared structures
- 7SS5 · Activated SgrAI endonuclease DNA-bound dimer with Ca2+ and intact primary site 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
- Every structure of UniProt Q9F6L0
- Elsewhere: RCSB PDB 7SS5 · PDBe 7SS5 · UniProt Q9F6L0
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