Research workbench
Sgrai with noncognate DNA bound
Analyse Sgrai with noncognate DNA bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DPG
- Type
- protein + DNA
- Length
- 709 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'- D(*DAP*DAP*DGP*DTP*DCP*DGP*DAP*DCP*DCP*DGP*DGP*DTP*DGP*DGP*DAP*DCP*DT )-3')…
- EC
- 3.1.21.4
- UniProt
- Q9F6L0
- Ligands
- CA
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | DNA (5'- D(*DAP*DAP*DGP*DTP*DCP*DGP*DAP*DCP*DCP*DGP*DGP*DTP*DGP*DGP*DAP*DCP*DT )-3') | dna | 17 | — | — |
| D | DNA (5'- D(*DAP*DAP*DGP*DTP*DCP*DGP*DAP*DCP*DCP*DGP*DGP*DTP*DGP*DGP*DAP*DCP*DT )-3') | dna | 16 | — | — |
| A, B | Sgrair restriction enzyme (EC 3.1.21.4) | protein | 338 | 49% helix, 12% strand | Q9F6L0 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains C, A, D, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 852 | 0.79 | 0.83 | 84 | empty |
| 2 | 321 | 0.73 | 0.86 | 49 | CA |
| 3 | 285 | 0.56 | 0.77 | 43 | empty |
| 4 | 73 | 0.30 | 0.74 | 14 | empty |
| 5 | 70 | 0.30 | 0.74 | 14 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1373 Ų buried · 12 hydrogen bonds · protein-protein
- D–A · 908 Ų buried · 24 hydrogen bonds · protein-nucleic
- C–B · 870 Ų buried · 23 hydrogen bonds · protein-nucleic
- C–D · 776 Ų buried · 66 hydrogen bonds · nucleic-nucleic
- D–B · 716 Ų buried · 15 hydrogen bonds · protein-nucleic
Compared structures
- 3DPG · SgrAI with noncognate DNA bound · the same entry in another collection · chain C against C, 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 3DPG · PDBe 3DPG · UniProt Q9F6L0
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.