MolNFT v1 · #49416 · protein + DNA
Crystal structure of T4 endonuclease VII N62D mutant in complex with a DNA holliday junction
2QNC · DNA (5'- D(*DCP*DG*DAP*DAP*DGP*DAP*DAP*DTP*DTP*DCP*DCP*DGP*D…: “Crystal structure of T4 endonuclease VII N62D mutant in complex with a DNA holliday junction”. X-ray diffraction, 2 ligands (MG, ZN), 10 pockets (best druggability…
- PDB
- 2QNC
- Type
- protein + DNA
- Length
- 407 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'- D(*DCP*DG*DAP*DAP*DGP*DAP*DAP*DTP*DTP*DCP*DCP*DGP*DGP*DAP*DTP*DTP*DAP…
- EC
- 3.1.22.4
- UniProt
- P13340
- Ligands
- MG, ZN
- Pockets
- 10 · best druggability 0.78
Structure
x-ray diffraction · 5 distinct chains · 54% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | DNA (5'- D(*DCP*DG*DAP*DAP*DGP*DAP*DAP*DTP*DTP*DCP*DCP*DGP*DGP*DAP*DTP*DTP*DAP *DGP*DGP*DGP*DAP*DTP*DCP*DC)-3') | dna | 22 | — | — |
| D | DNA (5'- D(*DGP*DGP*DAP*DTP*DCP*DCP*DCP*DTP*DAP*DAP*DGP*DCP*DTP*DCP*DCP*DAP*DT P*DCP*DGP*DAP*DTP*DGP*DTP*DG)-3') | dna | 24 | — | — |
| E | DNA (5'- D(*DCP*DAP*DCP*DAP*DTP*DCP*DGP*DAP*DTP*DGP*DGP*DAP*DGP*DCP*DCP*DGP*DC P*DTP*DAP*DGP*DGP*DCP*DCP*DT)-3') | dna | 24 | — | — |
| F | DNA (5'- D(*DAP*DGP*DGP*DCP*DCP*DTP*DAP*DGP*DCP*DGP*DTP*DCP*DCP*DGP*DGP*DAP*DA P*DTP*DTP*DCP*DTP*DTP*DCP*DG)-3') | dna | 23 | — | — |
| A, B | Recombination endonuclease VII (EC 3.1.22.4) | protein | 157 | 54% helix, 9% strand | P13340 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains F, B, D, A
- ZN · Zinc ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1039 | 0.78 | 0.80 | 68 | empty |
| 2 | 487 | 0.68 | 0.80 | 30 | empty |
| 3 | 416 | 0.64 | 0.78 | 38 | empty |
| 4 | 363 | 0.63 | 0.79 | 27 | empty |
| 5 | 190 | 0.43 | 0.74 | 20 | empty |
Interfaces
13 interfaces between chains.
- A–B · 3532 Ų buried · 33 hydrogen bonds · protein-protein
- D–E · 634 Ų buried · 62 hydrogen bonds · nucleic-nucleic
- D–A · 541 Ų buried · 21 hydrogen bonds · protein-nucleic
- F–B · 534 Ų buried · 18 hydrogen bonds · protein-nucleic
- C–F · 520 Ų buried · 43 hydrogen bonds · nucleic-nucleic
Compared structures
- 2QNC · Crystal structure of T4 Endonuclease VII N62D mutant in complex with a DNA Holliday… · 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 P13340
- Elsewhere: RCSB PDB 2QNC · PDBe 2QNC · UniProt P13340
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