Research workbench
Eukaryotic junction-resolving enzyme gen-1 binding with sodium
Analyse Eukaryotic junction-resolving enzyme gen-1 binding with sodium in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GRC
- Type
- protein + DNA
- Length
- 435 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
- 7 · best druggability 0.63
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nuclease-like protein | protein | 406 | 47% 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 · 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 | 357 | 0.63 | 0.79 | 35 | empty |
| 2 | 158 | 0.60 | 0.84 | 25 | empty |
| 3 | 257 | 0.58 | 0.78 | 27 | empty |
| 4 | 268 | 0.56 | 0.77 | 32 | empty |
| 5 | 85 | 0.54 | 0.85 | 22 | empty |
Interfaces
3 interfaces between chains.
- H–R · 652 Ų buried · 64 hydrogen bonds · nucleic-nucleic
- A–R · 410 Ų buried · 5 hydrogen bonds · protein-nucleic
- A–H · 404 Ų buried · 4 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 6 modified (engineered).
Compared structures
- 6GRC · eukaryotic junction-resolving enzyme GEN-1 binding with Sodium · 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 6GRC · PDBe 6GRC · UniProt G0RYN2
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