MolNFT v1 · #105707 · protein + DNA
Crystal structure of R.NGOAVII restriction endonuclease B3 domain with cognate DNA
4RD5 · Restriction endonuclease R.NGOVII: “Crystal structure of R.NGOAVII restriction endonuclease B3 domain with cognate DNA”. X-ray diffraction, 5 pockets (best druggability 0.50). MolNFT v1 #105707 on GenesisL1: 3D structure, binding…
- PDB
- 4RD5
- Type
- protein + DNA
- Length
- 379 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*CP*TP*AP*AP*GP*CP*GP*GP*CP*AP*AP*TP*CP…
- EC
- 3.1.21.4
- UniProt
- Q5F9M9
- Pockets
- 5 · best druggability 0.50
Structure
x-ray diffraction · 4 distinct chains · 27% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Restriction endonuclease R.NGOVII (EC 3.1.21.4) | protein | 160 | 26% helix, 26% strand | Q5F9M9 |
| B | Restriction endonuclease R.NGOVII (EC 3.1.21.4) | protein | 159 | 28% helix, 26% strand | Q5F9M9 |
| C, E | DNA (5'-D(*CP*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*GP*G)- 3') | dna | 15 | — | — |
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 | 220 | 0.50 | 0.76 | 28 | empty |
| 2 | 149 | 0.44 | 0.76 | 20 | empty |
| 3 | 163 | 0.42 | 0.75 | 19 | empty |
| 4 | 101 | 0.40 | 0.77 | 15 | empty |
| 5 | 67 | 0.36 | 0.78 | 13 | empty |
Interfaces
7 interfaces between chains.
- B–F · 762 Ų buried · 18 hydrogen bonds · protein-nucleic
- A–D · 696 Ų buried · 16 hydrogen bonds · protein-nucleic
- C–D · 653 Ų buried · 75 hydrogen bonds · nucleic-nucleic
- E–F · 649 Ų buried · 76 hydrogen bonds · nucleic-nucleic
- A–C · 581 Ų buried · 14 hydrogen bonds · protein-nucleic
Compared structures
- 4RD5 · 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 4RD5 · PDBe 4RD5 · UniProt Q5F9M9
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