MolNFT v1 · #72400 · protein + DNA
Sgrai bound to secondary site DNA and CA(II)
3N7B · Sgrair restriction enzyme: “Sgrai bound to secondary site DNA and CA(II)”. X-ray diffraction, 1 ligand (CA), 7 pockets (best druggability 0.73). MolNFT v1 #72400 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3N7B
- 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
- CA
- Pockets
- 7 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sgrair restriction enzyme (EC 3.1.21.4) | protein | 336 | 49% helix, 11% strand | Q9F6L0 |
| B | Sgrair restriction enzyme (EC 3.1.21.4) | protein | 333 | 47% helix, 11% 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
- CA · Calcium ion · metal · 3 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 307 | 0.73 | 0.86 | 40 | empty |
| 2 | 411 | 0.73 | 0.84 | 59 | empty |
| 3 | 317 | 0.58 | 0.77 | 38 | empty |
| 4 | 330 | 0.57 | 0.76 | 38 | empty |
| 5 | 85 | 0.41 | 0.79 | 19 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1349 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 888 Ų buried · 19 hydrogen bonds · protein-nucleic
- B–D · 885 Ų buried · 18 hydrogen bonds · protein-nucleic
- B–C · 731 Ų buried · 16 hydrogen bonds · protein-nucleic
- C–D · 727 Ų buried · 66 hydrogen bonds · nucleic-nucleic
Compared structures
- 3N7B · SgrAI bound to secondary site DNA and Ca(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 3N7B · PDBe 3N7B · UniProt Q9F6L0
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