MolNFT v1 · #103428 · protein
Caffeic acid O-methyltransferase from sorghum bicolor
4PGH: “Caffeic acid O-methyltransferase from sorghum bicolor”. X-ray diffraction, 1 ligand (SAM), 20 pockets (best druggability 0.79). MolNFT v1 #103428 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4PGH
- Type
- protein
- Length
- 1,422 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Caffeic acid O-methyltransferase
- EC
- 2.1.1.68
- UniProt
- C5YH12
- Ligands
- SAM
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Caffeic acid O-methyltransferase (EC 2.1.1.68) | protein | 354 | 47% helix, 19% strand | C5YH12 |
| B | Caffeic acid O-methyltransferase (EC 2.1.1.68) | protein | 357 | 46% helix, 17% strand | C5YH12 |
| C | Caffeic acid O-methyltransferase (EC 2.1.1.68) | protein | 353 | 46% helix, 16% strand | C5YH12 |
| D | Caffeic acid O-methyltransferase (EC 2.1.1.68) | protein | 358 | 44% helix, 16% strand | C5YH12 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 884 | 0.79 | 0.81 | 71 | SAM |
| 2 | 855 | 0.78 | 0.81 | 76 | SAM |
| 3 | 822 | 0.77 | 0.80 | 66 | SAM |
| 4 | 677 | 0.72 | 0.79 | 63 | SAM |
| 5 | 530 | 0.68 | 0.78 | 69 | empty |
Interfaces
5 interfaces between chains.
- C–D · 4740 Ų buried · 77 hydrogen bonds · protein-protein
- A–B · 4690 Ų buried · 73 hydrogen bonds · protein-protein
- A–D · 351 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 225 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 130 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4PGH · Caffeic acid O-methyltransferase from Sorghum bicolor · the same entry in another collection · chain A against A, TM-score 1.00
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 C5YH12
- Elsewhere: RCSB PDB 4PGH · PDBe 4PGH · UniProt C5YH12
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.