MolNFT v1 · #12461 · protein
Crystal structure of guanidinoacetate methyltransferase from rat liver: a template structure of protein arginine methyltransferase
1KHH: “Crystal structure of guanidinoacetate methyltransferase from rat liver: a template structure of protein…”. X-ray diffraction, 1 ligand (SAH), 2 pockets (best druggability 0.76). MolNFT v1 #12461 on GenesisL1: 3D structure, binding…
- PDB
- 1KHH
- Type
- protein
- Length
- 386 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Guanidinoacetate methyltransferase
- EC
- 2.1.1.2
- UniProt
- P10868
- Ligands
- SAH
- Pockets
- 2 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Guanidinoacetate methyltransferase (EC 2.1.1.2) | protein | 193 | 38% helix, 26% strand | P10868 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 340 | 0.76 | 0.87 | 53 | SAH |
| 2 | 189 | 0.71 | 0.88 | 45 | SAH |
Interfaces
1 interface between chains.
- A–B · 1216 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 1KHH · Crystal Structure of Guanidinoacetate Methyltransferase from Rat Liver: A Template… · the same entry in another collection · chain A against A, TM-score 1.00
- P10868 · AlphaFold monomer V2.0 prediction for guanidinoacetate N-methyltransferase (P10868) · a predicted model of the same protein · chain B 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 P10868
- Elsewhere: RCSB PDB 1KHH · PDBe 1KHH · UniProt P10868
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