Research workbench
Crystal structure of putative methyltransferase (ZP_00558420.1) from desulfitobacterium hafniense Y51 at 2.30 a resolution
Analyse Crystal structure of putative methyltransferase (ZP_00558420.1) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2QNE
- Type
- protein
- Length
- 951 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative methyltransferase
- UniProt
- Q24SP7
- Pockets
- 4 · best druggability 0.57
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative methyltransferase | protein | 476 | 49% helix, 15% strand | Q24SP7 |
| B | Putative methyltransferase | protein | 475 | 48% helix, 14% strand | Q24SP7 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 10 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 315 | 0.57 | 0.76 | 42 | EDO |
| 2 | 270 | 0.53 | 0.76 | 32 | EDO |
| 3 | 66 | 0.29 | 0.74 | 21 | empty |
| 4 | 54 | 0.25 | 0.72 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 5002 Ų buried · 65 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 38 modified (engineered).
Compared structures
- 2QNE · Crystal structure of putative methyltransferase (ZP_00558420.1) from Desulfitobacterium… · the same entry in another collection · chain A against A, TM-score 1.00
- Q24SP7 · AlphaFold monomer V2.0 prediction for glycine betaine methyltransferase (Q24SP7) · a predicted model of the same protein · chain A against A, TM-score 1.00
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 Q24SP7
- Elsewhere: RCSB PDB 2QNE · PDBe 2QNE · UniProt Q24SP7
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