MolNFT v1 · #117210 · protein
NTMT1 in complex with ypkria peptide
5E1D · N-terminal xaa-pro-lys N-methyltransferase 1: “NTMT1 in complex with ypkria peptide”. X-ray diffraction, 2 ligands (SAH, UNX), 6 pockets (best druggability 0.80). MolNFT v1 #117210 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5E1D
- Type
- protein
- Length
- 464 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-terminal xaa-pro-lys N-methyltransferase 1; RCC1
- EC
- 2.1.1.244
- UniProt
- Q9BV86
- Ligands
- SAH, UNX
- Pockets
- 6 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 41% 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 | 227 | 41% helix, 27% strand | Q9BV86 |
| B | N-terminal xaa-pro-lys N-methyltransferase 1 (EC 2.1.1.244) | protein | 225 | 42% helix, 26% strand | Q9BV86 |
| D, E | RCC1 | protein | 6 | 0% helix, 17% strand | — |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
- UNX · Unknown atom or ion · ion · 57 copies · chains A, D, B
- GOL · Glycerol · additive · 4 copies · chains A, D, B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 149 | 0.80 | 0.96 | 29 | SAH |
| 2 | 151 | 0.79 | 0.95 | 29 | SAH |
| 3 | 282 | 0.65 | 0.81 | 37 | GOL, UNX |
| 4 | 55 | 0.58 | 0.91 | 20 | GOL |
| 5 | 114 | 0.41 | 0.76 | 26 | UNX |
Interfaces
3 interfaces between chains.
- A–D · 538 Ų buried · 10 hydrogen bonds · protein-protein
- B–E · 525 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 508 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
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 5E1D · PDBe 5E1D · UniProt Q9BV86
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.