MolNFT v1 · #117730 · protein + DNA
Human PRDM9 allele-a znf domain with associated recombination hotspot DNA sequence III
5EH2 · DNA (5'- D(*AP*CP*AP*CP*GP*TP*GP*GP*CP*TP*AP*GP*GP*GP*AP*GP*…: “Human PRDM9 allele-a znf domain with associated recombination hotspot DNA sequence III”. X-ray diffraction, 1 ligand (ZN), 5 pockets (best druggability 0.64). MolNFT v1…
- PDB
- 5EH2
- Type
- protein + DNA
- Length
- 303 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'- D(*AP*CP*AP*CP*GP*TP*GP*GP*CP*TP*AP*GP*GP*GP*AP*GP*GP*CP*CP*TP*C)- 3'); DNA (5'…
- EC
- 2.1.1.43
- UniProt
- Q9NQV7
- Ligands
- ZN
- Pockets
- 5 · best druggability 0.64
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, A | DNA (5'- D(*AP*CP*AP*CP*GP*TP*GP*GP*CP*TP*AP*GP*GP*GP*AP*GP*GP*CP*CP*TP*C)- 3') | dna | 21 | — | — |
| D, B | DNA (5'- D(*TP*GP*AP*GP*GP*CP*CP*TP*CP*CP*CP*TP*AP*GP*CP*CP*AP*CP*GP*TP*G)- 3') | dna | 21 | — | — |
| E | Histone-lysine N-methyltransferase PRDM9 (EC 2.1.1.43) | protein | 110 | 40% helix, 15% strand | Q9NQV7 |
| F | Histone-lysine N-methyltransferase PRDM9 (EC 2.1.1.43) | protein | 109 | 39% helix, 15% strand | Q9NQV7 |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 338 | 0.64 | 0.80 | 28 | empty |
| 2 | 53 | 0.51 | 0.87 | 15 | empty |
| 3 | 92 | 0.49 | 0.83 | 15 | empty |
| 4 | 65 | 0.49 | 0.85 | 16 | empty |
| 5 | 58 | 0.24 | 0.72 | 11 | empty |
Interfaces
7 interfaces between chains.
- A–E · 1286 Ų buried · 35 hydrogen bonds · protein-nucleic
- C–F · 1210 Ų buried · 31 hydrogen bonds · protein-nucleic
- B–E · 969 Ų buried · 18 hydrogen bonds · protein-nucleic
- A–B · 944 Ų buried · 104 hydrogen bonds · nucleic-nucleic
- C–D · 936 Ų buried · 99 hydrogen bonds · nucleic-nucleic
Compared structures
- 5EH2 · Human PRDM9 allele-A ZnF Domain with Associated Recombination Hotspot DNA Sequence III · the same entry in another collection · chain F against F, 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 E against A, TM-score 0.84
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 5EH2 · PDBe 5EH2 · UniProt Q9NQV7
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