Research workbench
Sgrai bound to secondary site DNA and MG(II)
Analyse Sgrai bound to secondary site DNA and MG(II) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3N78
- Type
- protein + DNA
- Length
- 701 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sgrair restriction enzyme; DNA (5'-D(*AP*GP*TP*CP*CP*AP*CP*CP*GP*GP*GP*GP*GP*AP*CP*T)…
- EC
- 3.1.21.4
- UniProt
- Q9F6L0
- Ligands
- MG
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sgrair restriction enzyme (EC 3.1.21.4) | protein | 336 | 47% helix, 11% strand | Q9F6L0 |
| B | Sgrair restriction enzyme (EC 3.1.21.4) | protein | 333 | 45% helix, 13% strand | Q9F6L0 |
| C | DNA (5'-D(*AP*GP*TP*CP*CP*AP*CP*CP*GP*GP*GP*GP*GP*AP*CP*T)- 3') | dna | 16 | — | — |
| D | DNA (5'-D(*AP*GP*TP*CP*CP*CP*CP*CP*GP*GP*TP*GP*GP*AP*CP*T)- 3') | dna | 16 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 409 | 0.74 | 0.85 | 53 | empty |
| 2 | 386 | 0.73 | 0.84 | 53 | empty |
| 3 | 309 | 0.56 | 0.76 | 37 | empty |
| 4 | 264 | 0.53 | 0.76 | 37 | empty |
| 5 | 83 | 0.33 | 0.75 | 13 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1340 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 903 Ų buried · 24 hydrogen bonds · protein-nucleic
- B–D · 861 Ų buried · 19 hydrogen bonds · protein-nucleic
- B–C · 726 Ų buried · 14 hydrogen bonds · protein-nucleic
- A–D · 720 Ų buried · 19 hydrogen bonds · protein-nucleic
Compared structures
- 3N78 · SgrAI bound to Secondary Site DNA and Mg(II) · 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 3N78 · PDBe 3N78 · UniProt Q9F6L0
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