Research workbench
Crystal structure of human NRMT1 in complex with dimethylated fly H2B peptide and sah
Analyse Crystal structure of human NRMT1 in complex with dimethylated fly H2B peptide… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5CVE
- Type
- protein
- Length
- 471 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-terminal peptide from histone H2B
- EC
- 2.1.1.244
- UniProt
- Q9BV86, P02283
- Ligands
- SAH
- Pockets
- 3 · 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-terminal peptide from histone H2B | protein | 8 | 0% helix, 13% strand | P02283 |
| E | N-terminal peptide from histone H2B | protein | 6 | 0% helix, 17% strand | P02283 |
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
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 150 | 0.80 | 0.96 | 31 | SAH |
| 2 | 145 | 0.79 | 0.96 | 29 | SAH |
| 3 | 439 | 0.60 | 0.75 | 34 | empty |
Interfaces
3 interfaces between chains.
- B–E · 480 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 474 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 191 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- 5CVE · Crystal Structure of human NRMT1 in complex with dimethylated fly H2B peptide and SAH · 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
- P02283 · AlphaFold monomer V2.0 prediction for histone H2B (P02283) · a predicted model of the same protein · chain E against A, TM-score 0.37
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 P02283
- Elsewhere: RCSB PDB 5CVE · PDBe 5CVE · UniProt Q9BV86 · UniProt P02283
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