MolNFT v1 · #69416 · protein
Crystal structure of hpnmt in complex adohcy and adenine
3KPV · Phenylethanolamine N-methyltransferase: “Crystal structure of hpnmt in complex adohcy and adenine”. X-ray diffraction, 2 ligands (SAH, ADE), 4 pockets (best druggability 0.81). MolNFT v1 #69416 on GenesisL1: 3D structure, binding…
- PDB
- 3KPV
- Type
- protein
- Length
- 525 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
- SAH, ADE
- Pockets
- 4 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phenylethanolamine N-methyltransferase (EC 2.1.1.28) | protein | 257 | 37% helix, 25% strand | P11086 |
| B | Phenylethanolamine N-methyltransferase (EC 2.1.1.28) | protein | 268 | 39% helix, 23% strand | P11086 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
- ADE · Adenine · ligand · 2 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 203 | 0.81 | 0.94 | 40 | SAH, ADE |
| 2 | 131 | 0.77 | 0.95 | 28 | SAH |
| 3 | 77 | 0.75 | 0.97 | 21 | ADE |
| 4 | 57 | 0.44 | 0.83 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 544 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3KPV · Crystal Structure of hPNMT in Complex AdoHcy and Adenine · the same entry in another collection · chain B against B, TM-score 1.00
- P11086 · AlphaFold monomer V2.0 prediction for phenylethanolamine N-methyltransferase (P11086) · 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 P11086
- Elsewhere: RCSB PDB 3KPV · PDBe 3KPV · UniProt P11086
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