Research workbench
Crystal structure of the holliday junction-resolving enzyme GEN1 (wt) in complex with product DNA and MG2+ ion
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
- 5CO8
- Type
- protein + DNA
- Length
- 848 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (31-mer); Nuclease-like protein; DNA (5'-D(*AP*GP*AP*CP*TP*GP*CP*AP*GP*TP*TP*GP*AP*GP*…
- UniProt
- G0RYN2
- Ligands
- MG
- Pockets
- 18 · best druggability 0.77
Structure
x-ray diffraction · 5 distinct chains · 47% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| R | DNA (31-mer) | dna | 30 | — | — |
| C | Nuclease-like protein | protein | 397 | 47% helix, 14% strand | G0RYN2 |
| X | DNA (5'-D(*AP*GP*AP*CP*TP*GP*CP*AP*GP*TP*TP*GP*AP*GP*TP*C)- 3') | dna | 14 | — | — |
| A | Nuclease-like protein | protein | 393 | 46% helix, 15% strand | G0RYN2 |
| H | DNA (5'-D(*TP*GP*AP*GP*CP*GP*GP*TP*GP*GP*TP*TP*GP*GP*A)- 3') | dna | 14 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains C, X, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 885 | 0.77 | 0.80 | 48 | empty |
| 2 | 458 | 0.66 | 0.78 | 52 | MG |
| 3 | 192 | 0.62 | 0.84 | 23 | empty |
| 4 | 412 | 0.60 | 0.76 | 39 | MG |
| 5 | 188 | 0.59 | 0.82 | 25 | empty |
Interfaces
7 interfaces between chains.
- R–A · 755 Ų buried · 9 hydrogen bonds · protein-nucleic
- R–H · 631 Ų buried · 60 hydrogen bonds · nucleic-nucleic
- R–X · 627 Ų buried · 74 hydrogen bonds · nucleic-nucleic
- C–X · 474 Ų buried · 4 hydrogen bonds · protein-nucleic
- A–H · 387 Ų buried · 4 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 5CO8 · Crystal structure of the Holliday junction-resolving enzyme GEN1 (WT) in complex with… · the same entry in another collection · chain R against R, 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 5CO8 · PDBe 5CO8 · UniProt G0RYN2
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