MolNFT v1 · #97858 · protein
Haemonchus contortus phospholethanolamine N-methyltransferase 2 in complex with phosphomonomethylethanolamine and S-adenosylhomocysteine
4KRI: “Haemonchus contortus phospholethanolamine N-methyltransferase 2 in complex with phosphomonomethylethanolamine…”. X-ray diffraction, 2 ligands (SAH, 1SH), 16 pockets (best druggability 0.83). MolNFT v1 #97858 on GenesisL1: 3D…
- PDB
- 4KRI
- Type
- protein
- Length
- 1,281 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phospholethanolamine N-methyltransferase 2
- Ligands
- SAH, 1SH
- Pockets
- 16 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phospholethanolamine N-methyltransferase 2 | protein | 429 | 45% helix, 25% strand | — |
| B | Phospholethanolamine N-methyltransferase 2 | protein | 425 | 45% helix, 25% strand | — |
| C | Phospholethanolamine N-methyltransferase 2 | protein | 427 | 46% helix, 25% strand | — |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 3 copies · chains A, B, C
- 1SH · 2-(methylamino)ethyl dihydrogen phosphate · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 919 | 0.83 | 0.85 | 108 | empty |
| 2 | 179 | 0.81 | 0.96 | 43 | SAH, 1SH |
| 3 | 146 | 0.79 | 0.96 | 34 | SAH |
| 4 | 323 | 0.75 | 0.87 | 59 | SAH, 1SH |
| 5 | 522 | 0.62 | 0.75 | 47 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1387 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 333 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 233 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4KRI · Haemonchus contortus Phospholethanolamine N-methyltransferase 2 in complex with… · the same entry in another collection · 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
- Elsewhere: RCSB PDB 4KRI · PDBe 4KRI
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