MolNFT v1 · #154520 · protein
Crystal structure of human NRMT2 in complex with alpha-N- monomethylated human cenp-a peptide
6KDS · Alpha N-terminal protein methyltransferase 1B: “Crystal structure of human NRMT2 in complex with alpha-N- monomethylated human cenp-a peptide”. X-ray diffraction, 1 ligand (SAH), 1 pocket (best druggability 0.77). MolNFT v1 #154520…
- PDB
- 6KDS
- Type
- protein
- Length
- 227 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha N-terminal protein methyltransferase 1B; Cenp-a peptide
- EC
- 2.1.1.299
- UniProt
- Q5VVY1
- Ligands
- SAH
- Pockets
- 1 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha N-terminal protein methyltransferase 1B (EC 2.1.1.299) | protein | 221 | 40% helix, 27% strand | Q5VVY1 |
| E | Cenp-a peptide | protein | 6 | 0% helix, 17% strand | — |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · chains A, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 230 | 0.77 | 0.91 | 40 | SAH |
Interfaces
1 interface between chains.
- A–E · 586 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (methylation).
Compared structures
- 6KDS · Crystal structure of human NRMT2 in complex with alpha-N-monomethylated human CENP-A… · the same entry in another collection · chain A against A, TM-score 1.00
- Q5VVY1 · AlphaFold monomer V2.0 prediction for alpha N-terminal protein methyltransferase 1B… · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q5VVY1
- Elsewhere: RCSB PDB 6KDS · PDBe 6KDS · UniProt Q5VVY1
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