MolNFT v1 · #156398 · protein + DNA
Crystal structure of UHRF1 sra complexed with fully-mchg DNA.
6M2V · DNA (5'-D(*TP*CP*AP*CP*GP*(5CM)P*TP*GP*CP*GP*TP*GP*A)-3'): “Crystal structure of UHRF1 sra complexed with fully-mchg DNA.”. X-ray diffraction, 7 pockets (best druggability 0.70). MolNFT v1 #156398 on GenesisL1: 3D structure, binding…
- PDB
- 6M2V
- Type
- protein + DNA
- Length
- 414 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*TP*CP*AP*CP*GP*(5CM)P*TP*GP*CP*GP*TP*GP*A)-3'); E3 ubiquitin-protein ligase…
- EC
- 2.3.2.27
- UniProt
- Q8VDF2
- Pockets
- 7 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 21% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, D | DNA (5'-D(*TP*CP*AP*CP*GP*(5CM)P*TP*GP*CP*GP*TP*GP*A)-3') | dna | 13 | — | — |
| B | E3 ubiquitin-protein ligase UHRF1 (EC 2.3.2.27) | protein | 196 | 18% helix, 26% strand | Q8VDF2 |
| A | E3 ubiquitin-protein ligase UHRF1 (EC 2.3.2.27) | protein | 192 | 23% helix, 27% strand | Q8VDF2 |
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 725 | 0.70 | 0.77 | 48 | empty |
| 2 | 109 | 0.60 | 0.87 | 20 | empty |
| 3 | 179 | 0.58 | 0.82 | 19 | empty |
| 4 | 72 | 0.53 | 0.86 | 22 | empty |
| 5 | 63 | 0.31 | 0.76 | 18 | empty |
Interfaces
6 interfaces between chains.
- C–A · 610 Ų buried · 9 hydrogen bonds · protein-nucleic
- D–B · 593 Ų buried · 10 hydrogen bonds · protein-nucleic
- C–D · 572 Ų buried · 56 hydrogen bonds · nucleic-nucleic
- C–B · 340 Ų buried · 6 hydrogen bonds · protein-nucleic
- D–A · 323 Ų buried · 3 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 6M2V · Crystal structure of UHRF1 SRA complexed with fully-mCHG DNA. · the same entry in another collection · chain C against C, TM-score 1.00
- Q8VDF2 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase UHRF1 (Q8VDF2) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q8VDF2
- Elsewhere: RCSB PDB 6M2V · PDBe 6M2V · UniProt Q8VDF2
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