Research workbench
Crystal structure of bovine DNMT1 BAH1 domain in complex with H4K20ME3
Analyse Crystal structure of bovine DNMT1 BAH1 domain in complex with H4K20ME3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LMK
- Type
- protein
- Length
- 657 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (cytosine-5)-methyltransferase 1; Histone H4
- EC
- 2.1.1.37
- UniProt
- Q24K09, P62805
- Ligands
- ZN
- Pockets
- 5 · best druggability 0.39
Structure
x-ray diffraction · 6 distinct chains · 9% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA (cytosine-5)-methyltransferase 1 (EC 2.1.1.37) | protein | 158 | 9% helix, 41% strand | Q24K09 |
| B, C | DNA (cytosine-5)-methyltransferase 1 (EC 2.1.1.37) | protein | 156 | 8% helix, 37% strand | Q24K09 |
| D | DNA (cytosine-5)-methyltransferase 1 (EC 2.1.1.37) | protein | 155 | 10% helix, 41% strand | Q24K09 |
| F | Histone H4 | protein | 7 | 0% helix, 0% strand | P62805 |
| G, I | Histone H4 | protein | 8 | 0% helix, 0% strand | P62805 |
| H | Histone H4 | protein | 9 | 0% helix, 0% strand | P62805 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 94 | 0.39 | 0.76 | 21 | empty |
| 2 | 89 | 0.36 | 0.75 | 21 | empty |
| 3 | 53 | 0.32 | 0.77 | 13 | empty |
| 4 | 50 | 0.30 | 0.76 | 15 | empty |
| 5 | 55 | 0.24 | 0.72 | 12 | empty |
Interfaces
7 interfaces between chains.
- C–H · 633 Ų buried · 13 hydrogen bonds · protein-protein
- D–I · 541 Ų buried · 11 hydrogen bonds · protein-protein
- B–G · 535 Ų buried · 9 hydrogen bonds · protein-protein
- A–F · 514 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 231 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (methylation).
Compared structures
- 7LMK · Crystal structure of bovine DNMT1 BAH1 domain in complex with H4K20me3 · the same entry in another collection · chain I against I, TM-score 1.00
- Q24K09 · AlphaFold monomer V2.0 prediction for DNA (cytosine-5)-methyltransferase 1 (Q24K09) · a predicted model of the same protein · chain B against A, TM-score 0.73
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 Q24K09
- Every structure of UniProt P62805
- Elsewhere: RCSB PDB 7LMK · PDBe 7LMK · UniProt Q24K09 · UniProt P62805
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