MolNFT v1 · #91970 · protein
Crystal structure of zea mays ZMET2 in complex H3(1-32)K9ME2 peptide and sah
4FT4 · DNA (cytosine-5)-methyltransferase 1: “Crystal structure of zea mays ZMET2 in complex H3(1-32)K9ME2 peptide and sah”. X-ray diffraction, 1 ligand (SAH), 20 pockets (best druggability 0.76). MolNFT v1 #91970 on GenesisL1: 3D…
- PDB
- 4FT4
- Type
- protein
- Length
- 1,393 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (cytosine-5)-methyltransferase 1; H3(1-32)K9ME2 peptide
- EC
- 2.1.1.37
- UniProt
- Q9AXT8, P68431
- Ligands
- SAH
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 28% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | DNA (cytosine-5)-methyltransferase 1 (EC 2.1.1.37) | protein | 693 | 29% helix, 24% strand | Q9AXT8 |
| A | DNA (cytosine-5)-methyltransferase 1 (EC 2.1.1.37) | protein | 688 | 28% helix, 23% strand | Q9AXT8 |
| P | H3(1-32)K9ME2 peptide | protein | 7 | 0% helix, 0% strand | P68431 |
| Q | H3(1-32)K9ME2 peptide | protein | 5 | 0% helix, 0% strand | P68431 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 892 | 0.76 | 0.79 | 81 | SAH |
| 2 | 732 | 0.76 | 0.81 | 55 | empty |
| 3 | 738 | 0.73 | 0.79 | 73 | SAH |
| 4 | 466 | 0.63 | 0.76 | 57 | empty |
| 5 | 184 | 0.60 | 0.82 | 30 | empty |
Interfaces
3 interfaces between chains.
- B–A · 1773 Ų buried · 13 hydrogen bonds · protein-protein
- A–P · 494 Ų buried · 5 hydrogen bonds · protein-protein
- B–Q · 382 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (methylation).
Compared structures
- 4FT4 · crystal structure of Zea mays ZMET2 in complex H3(1-32)K9me2 peptide and SAH · the same entry in another collection · chain Q against Q, TM-score 1.00
- Q9AXT8 · AlphaFold monomer V2.0 prediction for DNA (cytosine-5)-methyltransferase 1 (Q9AXT8) · a predicted model of the same protein · chain B against A, TM-score 1.00
- P68431 · AlphaFold monomer V2.0 prediction for histone H3.1 (P68431) · a predicted model of the same protein · chain Q against A, TM-score 0.79
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 Q9AXT8
- Every structure of UniProt P68431
- Elsewhere: RCSB PDB 4FT4 · PDBe 4FT4 · UniProt Q9AXT8 · UniProt P68431
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