MolNFT v1 · #11561 · protein
Crystal structure analysis of human histamine methyltransferase (THR105 polymorphic variant) complexed with adohcy and histamine
1JQD · Histamine N-methyltransferase: “Crystal structure analysis of human histamine methyltransferase (THR105 polymorphic variant) complexed with…”. X-ray diffraction, 2 ligands (SAH, HSM), 3 pockets (best druggability 0.76). MolNFT v1…
- 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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