Research workbench
Human PRDM9 allele-a znf domain with associated recombination hotspot DNA sequence I
Analyse Human PRDM9 allele-a znf domain with associated recombination hotspot DNA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5EI9
- Type
- protein + DNA
- Length
- 305 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'- D(*AP*TP*CP*CP*AP*CP*GP*TP*GP*GP*CP*TP*AP*GP*GP*GP*AP*GP*GP*CP*C)- 3')…
- EC
- 2.1.1.43
- UniProt
- Q9NQV7
- Ligands
- ZN
- Pockets
- 3 · best druggability 0.60
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | DNA (5'- D(*AP*TP*CP*CP*AP*CP*GP*TP*GP*GP*CP*TP*AP*GP*GP*GP*AP*GP*GP*CP*C)- 3') | dna | 21 | — | — |
| F | Histone-lysine N-methyltransferase PRDM9 (EC 2.1.1.43) | protein | 110 | 38% helix, 15% strand | Q9NQV7 |
| E | Histone-lysine N-methyltransferase PRDM9 (EC 2.1.1.43) | protein | 111 | 39% helix, 14% strand | Q9NQV7 |
| B, D | DNA (5'- D(*TP*GP*GP*CP*CP*TP*CP*CP*CP*TP*AP*GP*CP*CP*AP*CP*GP*TP*GP*GP*A)- 3') | dna | 21 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains F, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 261 | 0.60 | 0.80 | 23 | empty |
| 2 | 73 | 0.48 | 0.84 | 17 | empty |
| 3 | 66 | 0.44 | 0.82 | 13 | empty |
Interfaces
7 interfaces between chains.
- F–C · 1303 Ų buried · 41 hydrogen bonds · protein-nucleic
- A–E · 1254 Ų buried · 32 hydrogen bonds · protein-nucleic
- C–D · 954 Ų buried · 112 hydrogen bonds · nucleic-nucleic
- A–B · 932 Ų buried · 113 hydrogen bonds · nucleic-nucleic
- F–D · 912 Ų buried · 18 hydrogen bonds · protein-nucleic
Compared structures
- 5EI9 · Human PRDM9 allele-A ZnF Domain with Associated Recombination Hotspot DNA Sequence I · the same entry in another collection · chain D against D, TM-score 1.00
- Q9NQV7 · AlphaFold monomer V2.0 prediction for histone-lysine N-methyltransferase PRDM9 (Q9NQV7) · a predicted model of the same protein · chain F against A, TM-score 0.87
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 Q9NQV7
- Elsewhere: RCSB PDB 5EI9 · PDBe 5EI9 · UniProt Q9NQV7
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.