MolNFT v1 · #160817 · protein
The structure of NTMT1 in complex with compound 6
6PVB · N-terminal xaa-pro-lys N-methyltransferase 1: “The structure of NTMT1 in complex with compound 6”. X-ray diffraction, 3 ligands (P2J, SAH, NH2), 2 pockets (best druggability 0.79). MolNFT v1 #160817 on GenesisL1: 3D structure…
- PDB
- 6PVB
- Type
- protein
- Length
- 231 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-terminal xaa-pro-lys N-methyltransferase 1; Amino…
- EC
- 2.1.1.244
- UniProt
- Q9BV86
- Ligands
- P2J, SAH, NH2
- Pockets
- 2 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | N-terminal xaa-pro-lys N-methyltransferase 1 (EC 2.1.1.244) | protein | 225 | 41% helix, 26% strand | Q9BV86 |
| A | Amino group-()-(2~{S})-2-azanylpropanal-()-isoleucine-()- arginine-()-lysine-()-proline-()-amino-acetaldehyde-()-9-(5-{[(3S)-3- amino-3-CARBOXYPROPYL](PENTYL)AMINO}-5-deoxy-beta-L- arabinofuranosyl)-9H-purin-6-amine | protein | 6 | 0% helix, 17% strand | — |
Ligands and binding sites
- P2J · 9-(5-{[(3S)-3-amino-3-carboxypropyl](pentyl)amino}-5-deoxy-beta-L-arabinofuranosyl)-9H-purin-6-amine · ligand · chains B, A
- SAH · S-adenosyl-L-homocysteine · ligand · chains B, A
- NH2 · Amino group · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 160 | 0.79 | 0.95 | 29 | SAH |
| 2 | 102 | 0.53 | 0.83 | 29 | empty |
Interfaces
1 interface between chains.
- B–A · 489 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent, 1 modified (covalent ligand, nonstandard).
Compared structures
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 Q9BV86
- Elsewhere: RCSB PDB 6PVB · PDBe 6PVB · UniProt Q9BV86
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