Research workbench
The structure of NTMT1 in complex with compound bm-30
Analyse The structure of NTMT1 in complex with compound bm-30 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WH8
- Type
- protein
- Length
- 458 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-terminal xaa-pro-lys N-methyltransferase 1; 4HP-pro-lys-arg-NH2, bm-30
- EC
- 2.1.1.244
- UniProt
- Q9BV86
- Ligands
- 4HP, SAH, NH2
- Pockets
- 4 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 41% 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 | 227 | 41% helix, 26% strand | Q9BV86 |
| A | N-terminal xaa-pro-lys N-methyltransferase 1 (EC 2.1.1.244) | protein | 225 | 42% helix, 27% strand | Q9BV86 |
| C, D | 4HP-pro-lys-arg-NH2, bm-30 | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
- 4HP · 4-hydroxyphenylacetate · ligand · 2 copies · chains B, C, A, D
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains B, A
- NH2 · Amino group · ion · 2 copies · chains B, C, A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 497 | 0.80 | 0.87 | 60 | 4HP, NH2, SAH |
| 2 | 277 | 0.80 | 0.92 | 52 | 4HP, SAH |
| 3 | 143 | 0.41 | 0.74 | 25 | empty |
| 4 | 105 | 0.38 | 0.75 | 19 | empty |
Interfaces
4 interfaces between chains.
- B–A · 508 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 358 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 358 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 20 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6WH8 · The structure of NTMT1 in complex with compound BM-30 · the same entry in another collection · chain A against A, 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 6WH8 · PDBe 6WH8 · UniProt Q9BV86
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