Research workbench
Crystal structure of human NRMT1 in complex with alpha-N- monomethylated human cenp-a peptide
Analyse Crystal structure of human NRMT1 in complex with alpha-N- monomethylated human… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6KDQ
- Type
- protein
- Length
- 468 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-terminal xaa-pro-lys N-methyltransferase 1; Cenp-a peptide
- EC
- 2.1.1.244
- UniProt
- Q9BV86
- Ligands
- SAH
- Pockets
- 5 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | N-terminal xaa-pro-lys N-methyltransferase 1 (EC 2.1.1.244) | protein | 229 | 41% helix, 27% strand | Q9BV86 |
| B | N-terminal xaa-pro-lys N-methyltransferase 1 (EC 2.1.1.244) | protein | 226 | 39% helix, 27% strand | Q9BV86 |
| E | Cenp-a peptide | protein | 6 | 0% helix, 17% strand | — |
| F | Cenp-a peptide | protein | 7 | 0% helix, 14% strand | — |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, E, B, F
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 | 142 | 0.79 | 0.96 | 28 | SAH |
| 2 | 153 | 0.79 | 0.95 | 31 | SAH |
| 3 | 70 | 0.62 | 0.91 | 21 | empty |
| 4 | 470 | 0.61 | 0.75 | 47 | empty |
| 5 | 68 | 0.60 | 0.91 | 22 | empty |
Interfaces
3 interfaces between chains.
- A–E · 563 Ų buried · 9 hydrogen bonds · protein-protein
- B–F · 548 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 177 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 modified (methylation).
Compared structures
- 6KDQ · Crystal structure of human NRMT1 in complex with alpha-N-monomethylated human CENP-A… · 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 B against A, TM-score 0.98
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 6KDQ · PDBe 6KDQ · UniProt Q9BV86
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