Research workbench
Mouse endonuclease G mutant H97A bound to a-DNA
Analyse Mouse endonuclease G mutant H97A bound to a-DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NJU
- Type
- protein + DNA
- Length
- 914 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endonuclease G, mitochondrial; DNA (5'-D(CCGGCGCCGG)-3')
- EC
- 3.1.30.-
- UniProt
- O08600
- Ligands
- MG, CL
- Pockets
- 16 · best druggability 0.75
Structure
x-ray diffraction · 5 distinct chains · 27% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endonuclease G, mitochondrial (EC 3.1.30.-) | protein | 223 | 26% helix, 30% strand | O08600 |
| B | Endonuclease G, mitochondrial (EC 3.1.30.-) | protein | 228 | 27% helix, 30% strand | O08600 |
| C | Endonuclease G, mitochondrial (EC 3.1.30.-) | protein | 224 | 27% helix, 31% strand | O08600 |
| D | Endonuclease G, mitochondrial (EC 3.1.30.-) | protein | 229 | 27% helix, 31% strand | O08600 |
| E | DNA (5'-D(CCGGCGCCGG)-3') | dna | 10 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 4 copies · chains A, C, D
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 187 | 0.75 | 0.91 | 34 | CL |
| 2 | 235 | 0.73 | 0.88 | 45 | empty |
| 3 | 54 | 0.69 | 0.97 | 26 | empty |
| 4 | 193 | 0.52 | 0.77 | 26 | MG |
| 5 | 160 | 0.49 | 0.78 | 22 | MG |
Interfaces
5 interfaces between chains.
- C–D · 2841 Ų buried · 38 hydrogen bonds · protein-protein
- A–B · 2764 Ų buried · 37 hydrogen bonds · protein-protein
- D–E · 109 Ų buried · 2 hydrogen bonds · protein-nucleic
- B–D · 67 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 45 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
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 O08600
- Elsewhere: RCSB PDB 6NJU · PDBe 6NJU · UniProt O08600
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