Research workbench
Human exog complexed with drp-containing DNA
Analyse Human exog complexed with drp-containing DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7R6V
- Type
- protein + DNA
- Length
- 1,237 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nuclease exog, mitochondrial; DNA (5'-D(*CP*TP*GP*AP*CP*GP*TP*GP*CP*G)-3'); DNA…
- EC
- 3.1.30.-
- UniProt
- Q9Y2C4
- Ligands
- MG, SO4
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 9 distinct chains · 31% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, I | Nuclease exog, mitochondrial (EC 3.1.30.-) | protein | 293 | 33% helix, 25% strand | Q9Y2C4 |
| E, G | Nuclease exog, mitochondrial (EC 3.1.30.-) | protein | 289 | 29% helix, 25% strand | Q9Y2C4 |
| F | DNA (5'-D(*CP*TP*GP*AP*CP*GP*TP*GP*CP*G)-3') | dna | 7 | — | — |
| H, K | DNA (5'-D(*CP*TP*GP*AP*CP*GP*TP*GP*CP*G)-3') | dna | 9 | — | — |
| B | DNA (5'-D(*CP*GP*CP*AP*CP*GP*TP*CP*AP*GP*AP*A)-3') | dna | 10 | — | — |
| A | DNA (5'-D(*CP*GP*CP*AP*CP*GP*TP*CP*AP*GP*AP*A)-3') | dna | 9 | — | — |
| J | DNA (5'-D(*CP*TP*GP*AP*CP*GP*TP*GP*CP*G)-3') | dna | 8 | — | — |
| L | DNA (5'-D(*CP*GP*CP*AP*CP*GP*TP*CP*AP*GP*AP*A)-3') | dna | 11 | — | — |
| M | DNA (5'-D(*CP*GP*CP*AP*CP*GP*TP*CP*AP*GP*AP*A)-3') | dna | 10 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 6 copies · chains D, F, E, H, I, K, G, J
- SO4 · Sulfate ion · ion · 3 copies · chains D, E, G, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1041 | 0.86 | 0.87 | 111 | empty |
| 2 | 410 | 0.84 | 0.92 | 63 | SO4 |
| 3 | 413 | 0.84 | 0.92 | 61 | empty |
| 4 | 942 | 0.76 | 0.79 | 61 | empty |
| 5 | 832 | 0.74 | 0.79 | 67 | empty |
Interfaces
20 interfaces between chains.
- D–E · 2588 Ų buried · 34 hydrogen bonds · protein-protein
- G–I · 2553 Ų buried · 35 hydrogen bonds · protein-protein
- I–K · 658 Ų buried · 18 hydrogen bonds · protein-nucleic
- E–H · 656 Ų buried · 20 hydrogen bonds · protein-nucleic
- G–J · 620 Ų buried · 19 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 7R6V · Human EXOG complexed with dRP-containing DNA · the same entry in another collection · chain M against M, 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 Q9Y2C4
- Elsewhere: RCSB PDB 7R6V · PDBe 7R6V · UniProt Q9Y2C4
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