Research workbench
Eukaryotic junction-resolving enzyme gen-1 binding with cesium
Analyse Eukaryotic junction-resolving enzyme gen-1 binding with cesium in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GRD
- Type
- protein + DNA
- Length
- 436 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
- CS, MG
- Pockets
- 5 · best druggability 0.60
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nuclease-like protein | protein | 407 | 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
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 256 | 0.60 | 0.80 | 29 | empty |
| 2 | 420 | 0.58 | 0.75 | 34 | empty |
| 3 | 278 | 0.57 | 0.77 | 28 | empty |
| 4 | 180 | 0.53 | 0.79 | 18 | empty |
| 5 | 52 | 0.33 | 0.77 | 13 | empty |
Interfaces
3 interfaces between chains.
- H–R · 632 Ų buried · 63 hydrogen bonds · nucleic-nucleic
- A–H · 361 Ų buried · 6 hydrogen bonds · protein-nucleic
- A–R · 290 Ų buried · 8 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 7 modified (engineered).
Compared structures
- 6GRD · eukaryotic junction-resolving enzyme GEN-1 binding with Cesium · 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 6GRD · PDBe 6GRD · UniProt G0RYN2
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