Research workbench
Crystal structure analysis of human histamine methyltransferase (THR105 polymorphic variant) complexed with adohcy and histamine
Analyse Crystal structure analysis of human histamine methyltransferase (THR105… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1JQD
- Type
- protein
- Length
- 574 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histamine N-methyltransferase
- EC
- 2.1.1.8
- UniProt
- P50135
- Ligands
- SAH, HSM
- Pockets
- 3 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histamine N-methyltransferase (EC 2.1.1.8) | protein | 286 | 44% helix, 23% strand | P50135 |
| B | Histamine N-methyltransferase (EC 2.1.1.8) | protein | 288 | 45% helix, 24% strand | P50135 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
- HSM · Histamine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 566 | 0.76 | 0.83 | 57 | SAH, HSM |
| 2 | 706 | 0.76 | 0.81 | 60 | SAH, HSM |
| 3 | 560 | 0.69 | 0.78 | 58 | empty |
Interfaces
1 interface between chains.
- A–B · 431 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 1JQD · Crystal Structure Analysis of Human Histamine Methyltransferase (Thr105 Polymorphic… · the same entry in another collection · chain B against B, TM-score 1.00
- P50135 · AlphaFold monomer V2.0 prediction for histamine N-methyltransferase (P50135) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P50135
- Elsewhere: RCSB PDB 1JQD · PDBe 1JQD · UniProt P50135
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