Research workbench
Human PRDM9 allele-a znf domain with associated recombination hotspot DNA sequence II
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
- 5EGB
- Type
- protein + DNA
- Length
- 153 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'- D(*AP*CP*CP*AP*CP*GP*TP*GP*GP*CP*TP*AP*GP*GP*GP*AP*GP*GP*CP*CP*T)- 3'); DNA (5'…
- EC
- 2.1.1.43
- UniProt
- Q9NQV7
- Ligands
- ZN
- Pockets
- 2 · best druggability 0.54
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | DNA (5'- D(*AP*CP*CP*AP*CP*GP*TP*GP*GP*CP*TP*AP*GP*GP*GP*AP*GP*GP*CP*CP*T)- 3') | dna | 21 | — | — |
| D | DNA (5'- D(*TP*AP*GP*GP*CP*CP*TP*CP*CP*CP*TP*AP*GP*CP*CP*AP*CP*GP*TP*GP*G)- 3') | dna | 21 | — | — |
| A | Histone-lysine N-methyltransferase PRDM9 (EC 2.1.1.43) | protein | 111 | 39% helix, 14% strand | Q9NQV7 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 93 | 0.54 | 0.85 | 15 | empty |
| 2 | 52 | 0.42 | 0.83 | 13 | empty |
Interfaces
3 interfaces between chains.
- C–A · 1269 Ų buried · 31 hydrogen bonds · protein-nucleic
- D–A · 967 Ų buried · 22 hydrogen bonds · protein-nucleic
- C–D · 940 Ų buried · 97 hydrogen bonds · nucleic-nucleic
Compared structures
- 5EGB · Human PRDM9 allele-A ZnF Domain with Associated Recombination Hotspot DNA Sequence II · the same entry in another collection · chain C against C, 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 A against A, TM-score 0.82
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 5EGB · PDBe 5EGB · UniProt Q9NQV7
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