Research workbench
Crystal structure of the holliday junction-resolving enzyme GEN1 (wt) in complex with product DNA, MG2+ and MN2+ ions
Analyse Crystal structure of the holliday junction-resolving enzyme GEN1 (wt) in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5CNQ
- Type
- protein + DNA
- Length
- 421 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nuclease-like protein; R; DNA (5'-D(*TP*GP*AP*GP*CP*GP*GP*TP*GP*GP*TP*TP*GP*GP*T)- 3')
- UniProt
- G0RYN2
- Ligands
- MN
- Pockets
- 7 · best druggability 0.61
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nuclease-like protein | protein | 392 | 46% helix, 14% strand | G0RYN2 |
| R | R | dna | 15 | — | — |
| H | DNA (5'-D(*TP*GP*AP*GP*CP*GP*GP*TP*GP*GP*TP*TP*GP*GP*T)- 3') | dna | 14 | — | — |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 2 copies · chains A, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 224 | 0.61 | 0.82 | 26 | empty |
| 2 | 343 | 0.60 | 0.78 | 30 | empty |
| 3 | 297 | 0.59 | 0.78 | 31 | empty |
| 4 | 203 | 0.56 | 0.79 | 24 | empty |
| 5 | 86 | 0.53 | 0.85 | 27 | empty |
Interfaces
3 interfaces between chains.
- R–H · 659 Ų buried · 76 hydrogen bonds · nucleic-nucleic
- A–H · 459 Ų buried · 6 hydrogen bonds · protein-nucleic
- A–R · 366 Ų buried · 6 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 7 modified (engineered).
Compared structures
- 5CNQ · Crystal structure of the Holliday junction-resolving enzyme GEN1 (WT) in complex with… · 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 G0RYN2
- Elsewhere: RCSB PDB 5CNQ · PDBe 5CNQ · UniProt G0RYN2
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