MolNFT v1 · #115832 · protein
Crystal structure of human NRMT1 in complex with alpha-N-dimethylated human cenp-a peptide
5CVD · N-terminal xaa-pro-lys N-methyltransferase 1: “Crystal structure of human NRMT1 in complex with alpha-N-dimethylated human cenp-a peptide”. X-ray diffraction, 1 ligand (SAH), 5 pockets (best druggability 0.80). MolNFT v1 #115832 on…
- PDB
- 5CVD
- Type
- protein
- Length
- 470 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-terminal xaa-pro-lys N-methyltransferase 1; N-teminal peptide from histone H3-like…
- EC
- 2.1.1.244
- UniProt
- Q9BV86, P49450
- Ligands
- SAH
- Pockets
- 5 · best druggability 0.80
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 | 231 | 40% helix, 26% strand | Q9BV86 |
| B | N-terminal xaa-pro-lys N-methyltransferase 1 (EC 2.1.1.244) | protein | 226 | 40% helix, 27% strand | Q9BV86 |
| D | N-teminal peptide from histone H3-like centromeric protein a | protein | 6 | 0% helix, 17% strand | P49450 |
| E | N-teminal peptide from histone H3-like centromeric protein a | protein | 7 | 0% helix, 14% strand | P49450 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, D, B, E
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 | 147 | 0.80 | 0.96 | 29 | SAH |
| 2 | 144 | 0.79 | 0.96 | 29 | SAH |
| 3 | 72 | 0.62 | 0.91 | 23 | empty |
| 4 | 73 | 0.61 | 0.90 | 23 | empty |
| 5 | 464 | 0.59 | 0.74 | 41 | empty |
Interfaces
3 interfaces between chains.
- A–D · 558 Ų buried · 9 hydrogen bonds · protein-protein
- B–E · 542 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 190 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- 5CVD · Crystal structure of human NRMT1 in complex with alpha-N-dimethylated human CENP-A peptide · the same entry in another collection · chain E against E, 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
- P49450 · AlphaFold monomer V2.0 prediction for histone H3-like centromeric protein a (P49450) · a predicted model of the same protein · chain D against A, TM-score 0.58
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
- Every structure of UniProt P49450
- Elsewhere: RCSB PDB 5CVD · PDBe 5CVD · UniProt Q9BV86 · UniProt P49450
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