Research workbench
Eukaryotic junction-resolving enzyme gen-1 binding with potassium
Analyse Eukaryotic junction-resolving enzyme gen-1 binding with potassium in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GRB
- Type
- protein + DNA
- Length
- 427 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nuclease-like protein; DNA (5'-D(*TP*GP*AP*GP*CP*GP*GP*TP*GP*GP*TP*TP*GP*GP*T)- 3'); DNA…
- UniProt
- G0RYN2
- Ligands
- MG
- Pockets
- 6 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nuclease-like protein | protein | 398 | 49% helix, 14% strand | G0RYN2 |
| H | DNA (5'-D(*TP*GP*AP*GP*CP*GP*GP*TP*GP*GP*TP*TP*GP*GP*T)- 3') | dna | 14 | — | — |
| R | DNA (5'-D(*TP*AP*CP*CP*CP*AP*CP*CP*AP*CP*CP*GP*CP*TP*CP*A)- 3') | dna | 15 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 503 | 0.66 | 0.77 | 51 | empty |
| 2 | 402 | 0.60 | 0.76 | 33 | empty |
| 3 | 72 | 0.56 | 0.88 | 21 | empty |
| 4 | 145 | 0.52 | 0.81 | 21 | empty |
| 5 | 71 | 0.31 | 0.74 | 14 | empty |
Interfaces
3 interfaces between chains.
- H–R · 668 Ų buried · 72 hydrogen bonds · nucleic-nucleic
- A–H · 386 Ų buried · 3 hydrogen bonds · protein-nucleic
- A–R · 291 Ų buried · 5 hydrogen bonds · protein-nucleic
Compared structures
- 6GRB · eukaryotic junction-resolving enzyme GEN-1 binding with Potassium · 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 6GRB · PDBe 6GRB · UniProt G0RYN2
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