Research workbench
Crystal structure of se-substituted zea mays ZMET2 in complex with sah
Analyse Crystal structure of se-substituted zea mays ZMET2 in complex with sah in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4FSX
- Type
- protein
- Length
- 1,355 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (cytosine-5)-methyltransferase 1
- EC
- 2.1.1.37
- UniProt
- Q9AXT8
- Ligands
- SAH
- Pockets
- 19 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA (cytosine-5)-methyltransferase 1 (EC 2.1.1.37) | protein | 680 | 26% helix, 21% strand | Q9AXT8 |
| B | DNA (cytosine-5)-methyltransferase 1 (EC 2.1.1.37) | protein | 675 | 27% helix, 20% strand | Q9AXT8 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 371 | 0.64 | 0.79 | 49 | SAH |
| 2 | 430 | 0.63 | 0.77 | 55 | SAH |
| 3 | 202 | 0.62 | 0.82 | 32 | empty |
| 4 | 112 | 0.56 | 0.84 | 36 | empty |
| 5 | 85 | 0.55 | 0.86 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 687 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 30 modified (engineered).
Compared structures
- 4FSX · crystal structure of Se-substituted Zea mays ZMET2 in complex with SAH · the same entry in another collection · chain A against A, 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 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 Q9AXT8
- Elsewhere: RCSB PDB 4FSX · PDBe 4FSX · UniProt Q9AXT8
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