Research workbench
Structure of human pnmt complexed with cofactor product adohcy and inhibitor SK&F 64139
Analyse Structure of human pnmt complexed with cofactor product adohcy and inhibitor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1YZ3
- Type
- protein
- Length
- 530 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phenylethanolamine N-methyltransferase
- EC
- 2.1.1.28
- UniProt
- P11086
- Ligands
- SKA, SAH
- Pockets
- 6 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phenylethanolamine N-methyltransferase (EC 2.1.1.28) | protein | 263 | 36% helix, 23% strand | P11086 |
| B | Phenylethanolamine N-methyltransferase (EC 2.1.1.28) | protein | 267 | 38% helix, 24% strand | P11086 |
Ligands and binding sites
- SKA · 7,8-dichloro-1,2,3,4-tetrahydroisoquinoline · ligand · 2 copies · chains A, B
- 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
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 205 | 0.82 | 0.95 | 41 | SKA, SAH |
| 2 | 158 | 0.77 | 0.93 | 31 | SAH |
| 3 | 75 | 0.75 | 0.98 | 17 | SKA |
| 4 | 128 | 0.49 | 0.79 | 30 | empty |
| 5 | 82 | 0.45 | 0.81 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 618 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 1YZ3 · Structure of human pnmt complexed with cofactor product adohcy and inhibitor SK&F 64139 · the same entry in another collection · chain A against A, TM-score 1.00
- 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 1YZ3 · PDBe 1YZ3 · UniProt P11086
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