MolNFT v1 · #49419 · protein + DNA
Crystal structure of T4 endonuclease VII H43N mutant in complex with heteroduplex DNA containing base mismatches
2QNF · DNA (5'- D(*DCP*DAP*DCP*DAP*DTP*DCP*DGP*DAP*DTP*DGP*DGP*DAP*…: “Crystal structure of T4 endonuclease VII H43N mutant in complex with heteroduplex DNA containing base…”. X-ray diffraction, 1 ligand (ZN), 5 pockets (best druggability…
- PDB
- 2QNF
- Type
- protein + DNA
- Length
- 378 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'- D(*DCP*DAP*DCP*DAP*DTP*DCP*DGP*DAP*DTP*DGP*DGP*DAP*DGP*DCP*DCP*DG)- 3'); DNA…
- EC
- 3.1.22.4
- UniProt
- P13340
- Ligands
- ZN
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 5 distinct chains · 50% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | DNA (5'- D(*DCP*DAP*DCP*DAP*DTP*DCP*DGP*DAP*DTP*DGP*DGP*DAP*DGP*DCP*DCP*DG)- 3') | dna | 16 | — | — |
| D | DNA (5'- D(*DGP*DCP*DGP*DCP*DTP*DCP*DCP*DAP*DTP*DCP*DGP*DAP*DTP*DGP*DTP*DG)- 3') | dna | 16 | — | — |
| E | DNA (5'- D(*DCP*DGP*DGP*DCP*DTP*DCP*DCP*DAP*DTP*DCP*DGP*DAP*DTP*DGP*DTP*DG)- 3') | dna | 16 | — | — |
| F | DNA (5'- D(*DCP*DAP*DCP*DAP*DTP*DCP*DGP*DAP*DTP*DGP*DGP*DAP*DGP*DCP*DGP*DC)- 3') | dna | 16 | — | — |
| A, B | Recombination endonuclease VII (EC 3.1.22.4) | protein | 157 | 50% helix, 9% strand | P13340 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 951 | 0.75 | 0.79 | 74 | empty |
| 2 | 894 | 0.75 | 0.79 | 70 | empty |
| 3 | 60 | 0.39 | 0.80 | 17 | empty |
| 4 | 133 | 0.38 | 0.74 | 16 | empty |
| 5 | 124 | 0.35 | 0.72 | 15 | empty |
Interfaces
11 interfaces between chains.
- A–B · 3630 Ų buried · 32 hydrogen bonds · protein-protein
- C–D · 708 Ų buried · 57 hydrogen bonds · nucleic-nucleic
- E–F · 703 Ų buried · 59 hydrogen bonds · nucleic-nucleic
- E–B · 294 Ų buried · 8 hydrogen bonds · protein-nucleic
- D–A · 282 Ų buried · 8 hydrogen bonds · protein-nucleic
Compared structures
- 2QNF · Crystal structure of T4 Endonuclease VII H43N mutant in complex with heteroduplex DNA… · 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 2QNF · PDBe 2QNF · UniProt P13340
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