Research workbench
Crystal structure of T4 endonuclease VII H43N mutant in complex with heteroduplex DNA containing base mismatches
Analyse Crystal structure of T4 endonuclease VII H43N mutant in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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