Research workbench
Crystal structure of human phenylethanolamine N-methyltransferase (PNMT) in complex with (2S)-2-amino-4-(((5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl)methyl)(4-(7,8-dichloro-1,2,3,4-tetrahydroisoquinolin-4-yl)butyl)amino)butanoic acid and AdoHcy (SAH)
Analyse Crystal structure of human phenylethanolamine N-methyltransferase (PNMT) in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7TWU
- Type
- protein
- Length
- 526 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.1
- Source
- Homo sapiens
- Molecule
- Phenylethanolamine N-methyltransferase
- EC
- 2.1.1.28
- UniProt
- P11086
- Ligands
- SAH, KNX, CD
- Pockets
- 6 · best druggability 0.83
Structure
x-ray diffraction · resolution 2.1 · 2 distinct chains · 38% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phenylethanolamine N-methyltransferase (EC 2.1.1.28) | protein | 260 | 38% helix, 26% strand | P11086 |
| B | Phenylethanolamine N-methyltransferase (EC 2.1.1.28) | protein | 266 | 38% helix, 26% strand | P11086 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · chains A
- KNX · 5'-([(3S)-3-amino-3-carboxypropyl]{4-[(4R)-7,8-dichloro-1,2,3,4-tetrahydroisoquinolin-4-yl]butyl}amino)-5'-deoxyadenosine · ligand · chains B
- CD · Cadmium ion · metal · chains A
- EDO · 1,2-ethanediol · additive · 15 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 236 | 0.83 | 0.95 | 42 | KNX |
| 2 | 134 | 0.77 | 0.95 | 28 | SAH |
| 3 | 69 | 0.74 | 0.98 | 17 | CD, EDO |
| 4 | 148 | 0.54 | 0.81 | 23 | EDO |
| 5 | 120 | 0.46 | 0.79 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 529 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- P11086 · AlphaFold monomer V2.0 prediction for phenylethanolamine N-methyltransferase (P11086) · a predicted model of the same protein · chain B 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 P11086
- Elsewhere: RCSB PDB 7TWU · PDBe 7TWU · UniProt P11086
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