Research workbench
Atomic structure of the eukaryotic intramembrane RAS methyltransferase icmt (isoprenylcysteine carboxyl methyltransferase), in complex with a monobody
Analyse Atomic structure of the eukaryotic intramembrane RAS methyltransferase icmt… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5V7P
- Type
- protein
- Length
- 375 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein-S-isoprenylcysteine O-methyltransferase; Monobody
- EC
- 2.1.1.100
- UniProt
- D6WJ77
- Ligands
- D10, MPG, SAH
- Pockets
- 3 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 58% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein-S-isoprenylcysteine O-methyltransferase (EC 2.1.1.100) | protein | 280 | 76% helix, 0% strand | D6WJ77 |
| D | Monobody | protein | 95 | 3% helix, 53% strand | — |
Ligands and binding sites
- D10 · Decane · ligand · 11 copies · chains A
- MPG · [(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate · ligand · 10 copies · chains A, D
- SAH · S-adenosyl-L-homocysteine · ligand · chains A
- UND · Undecane · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 728 | 0.84 | 0.87 | 79 | SAH, D10, MPG |
| 2 | 170 | 0.46 | 0.75 | 25 | D10, MPG |
| 3 | 50 | 0.27 | 0.74 | 13 | empty |
Interfaces
1 interface between chains.
- A–D · 873 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5V7P · Atomic structure of the eukaryotic intramembrane Ras methyltransferase ICMT… · the same entry in another collection · chain A against A, TM-score 1.00
- D6WJ77 · AlphaFold monomer V2.0 prediction for protein-S-isoprenylcysteine O-methyltransferase… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 D6WJ77
- Elsewhere: RCSB PDB 5V7P · PDBe 5V7P · UniProt D6WJ77
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.