Research workbench
Crystal structure of R.NGOAVII restriction endonuclease B3 domain with cognate DNA
Analyse Crystal structure of R.NGOAVII restriction endonuclease B3 domain with cognate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RDM
- Type
- protein + DNA
- Length
- 388 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Restriction endonuclease R.NGOVII; DNA (5'-D(*CP*CP*TP*AP*AP*GP*CP*GP*GP*CP*AP*AP*TP*CP*C)…
- EC
- 3.1.21.4
- UniProt
- Q5F9M9
- Ligands
- SO4
- Pockets
- 5 · best druggability 0.57
Structure
x-ray diffraction · 5 distinct chains · 26% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Restriction endonuclease R.NGOVII (EC 3.1.21.4) | protein | 165 | 25% helix, 25% strand | Q5F9M9 |
| B | Restriction endonuclease R.NGOVII (EC 3.1.21.4) | protein | 164 | 26% helix, 26% strand | Q5F9M9 |
| C | DNA (5'-D(*CP*CP*TP*AP*AP*GP*CP*GP*GP*CP*AP*AP*TP*CP*C)-3) ' | dna | 15 | — | — |
| D, F | DNA (5'-D(*GP*GP*GP*AP*TP*TP*GP*CP*CP*GP*CP*TP*TP*AP*G)-3) ' | dna | 15 | — | — |
| E | DNA (5'-D(*CP*CP*TP*AP*AP*GP*CP*GP*GP*CP*AP*AP*TP*CP*C)-3) ' | dna | 14 | — | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 439 | 0.57 | 0.74 | 50 | empty |
| 2 | 180 | 0.43 | 0.74 | 24 | empty |
| 3 | 188 | 0.43 | 0.74 | 24 | empty |
| 4 | 80 | 0.40 | 0.79 | 13 | empty |
| 5 | 104 | 0.39 | 0.76 | 19 | empty |
Interfaces
7 interfaces between chains.
- A–D · 774 Ų buried · 16 hydrogen bonds · protein-nucleic
- B–F · 707 Ų buried · 13 hydrogen bonds · protein-nucleic
- E–F · 670 Ų buried · 69 hydrogen bonds · nucleic-nucleic
- C–D · 668 Ų buried · 66 hydrogen bonds · nucleic-nucleic
- A–C · 554 Ų buried · 13 hydrogen bonds · protein-nucleic
Compared structures
- 4RDM · Crystal structure of R.NgoAVII restriction endonuclease B3 domain with cognate 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 Q5F9M9
- Elsewhere: RCSB PDB 4RDM · PDBe 4RDM · UniProt Q5F9M9
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