Research workbench
The structure of NTMT1 in complex with compound DC1-13
Analyse The structure of NTMT1 in complex with compound DC1-13 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7K3D
- Type
- protein
- Length
- 442 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-terminal xaa-pro-lys N-methyltransferase 1
- EC
- 2.1.1.244
- UniProt
- Q9BV86
- Ligands
- SAH, VWP
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A | N-terminal xaa-pro-lys N-methyltransferase 1 (EC 2.1.1.244) | protein | 221 | 39% helix, 27% strand | Q9BV86 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains B, A
- VWP · N~2~-{(2S)-1-[(naphthalen-1-yl)acetyl]-2,5-dihydro-1H-pyrrole-2-carbonyl}-L-lysyl-L-argininamide · ligand · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 451 | 0.78 | 0.86 | 51 | SAH, VWP |
| 2 | 446 | 0.78 | 0.86 | 49 | SAH, VWP |
| 3 | 474 | 0.75 | 0.84 | 46 | empty |
| 4 | 73 | 0.58 | 0.88 | 16 | empty |
| 5 | 136 | 0.56 | 0.83 | 21 | empty |
Interfaces
1 interface between chains.
- B–A · 928 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7K3D · The structure of NTMT1 in complex with compound DC1-13 · the same entry in another collection · chain B against B, TM-score 1.00
- Q9BV86 · AlphaFold monomer V2.0 prediction for N-terminal xaa-pro-lys N-methyltransferase 1… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 7K3D · PDBe 7K3D · UniProt Q9BV86
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