MolNFT v1 · #186224 · protein + DNA
Human exog complexed with drp-containing DNA
7R6T · Nuclease exog, mitochondrial: “Human exog complexed with drp-containing DNA”. X-ray diffraction, 2 ligands (MG, NA), 15 pockets (best druggability 0.83). MolNFT v1 #186224 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 7R6T
- Type
- protein + DNA
- Length
- 915 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nuclease exog, mitochondrial; DNA (5'-D(3DR)P*CP*TP*GP*AP*CP*GP*TP*GP*C)-3'); DNA…
- EC
- 3.1.30.-
- UniProt
- Q9Y2C4
- Ligands
- MG, NA
- Pockets
- 15 · best druggability 0.83
Structure
x-ray diffraction · 9 distinct chains · 26% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | Nuclease exog, mitochondrial (EC 3.1.30.-) | protein | 287 | 25% helix, 25% strand | Q9Y2C4 |
| F | DNA (5'-D(3DR)P*CP*TP*GP*AP*CP*GP*TP*GP*C)-3') | dna | 9 | — | — |
| A | DNA (5'-D(*CP*GP*CP*AP*CP*GP*TP*CP*AP*GP*A)-3') | dna | 9 | — | — |
| C | Nuclease exog, mitochondrial (EC 3.1.30.-) | protein | 290 | 32% helix, 25% strand | Q9Y2C4 |
| E | DNA (5'-D(3DR)P*CP*TP*GP*AP*CP*GP*TP*GP*C)-3') | dna | 9 | — | — |
| B | DNA (5'-D(*CP*GP*CP*AP*CP*GP*TP*CP*AP*GP*A)-3') | dna | 9 | — | — |
| L | Nuclease exog, mitochondrial (EC 3.1.30.-) | protein | 288 | 23% helix, 26% strand | Q9Y2C4 |
| M | DNA (5'-D(3DR)P*CP*TP*GP*AP*CP*GP*TP*GP*C)-3') | dna | 7 | — | — |
| K | DNA (5'-D(*CP*GP*CP*AP*CP*GP*TP*CP*AP*GP*A)-3') | dna | 7 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains D, F, A, C, E, L, M
- NA · Sodium ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 360 | 0.83 | 0.92 | 56 | empty |
| 2 | 975 | 0.75 | 0.78 | 81 | empty |
| 3 | 660 | 0.74 | 0.80 | 51 | empty |
| 4 | 399 | 0.60 | 0.76 | 43 | empty |
| 5 | 424 | 0.60 | 0.75 | 36 | empty |
Interfaces
13 interfaces between chains.
- D–C · 2472 Ų buried · 33 hydrogen bonds · protein-protein
- C–E · 710 Ų buried · 19 hydrogen bonds · protein-nucleic
- D–F · 688 Ų buried · 20 hydrogen bonds · protein-nucleic
- L–M · 538 Ų buried · 12 hydrogen bonds · protein-nucleic
- F–A · 477 Ų buried · 34 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 disulfide, 1 modified (disulfide, nucleotide modification).
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 Q9Y2C4
- Elsewhere: RCSB PDB 7R6T · PDBe 7R6T · UniProt Q9Y2C4
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