Research workbench
Crystal structure of O-methyltransferase family 2 protein PLIM_1147 from planctomyces limnophilus dsm 3776 complex with apigenin
Analyse Crystal structure of O-methyltransferase family 2 protein PLIM_1147 from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5I2H
- Type
- protein
- Length
- 663 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- O-methyltransferase family 2
- UniProt
- D5STZ7
- Ligands
- AGI
- Pockets
- 4 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | O-methyltransferase family 2 | protein | 335 | 49% helix, 15% strand | D5STZ7 |
| B | O-methyltransferase family 2 | protein | 328 | 49% helix, 16% strand | D5STZ7 |
Ligands and binding sites
- AGI · 5,7-dihydroxy-2-(4-hydroxyphenyl)-4H-chromen-4-one · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 10 copies · chains A, B
- FMT · Formic acid · additive · 8 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1157 | 0.78 | 0.80 | 104 | AGI, EDO, FMT |
| 2 | 145 | 0.46 | 0.77 | 18 | EDO |
| 3 | 115 | 0.39 | 0.75 | 24 | empty |
| 4 | 91 | 0.32 | 0.73 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1927 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 modified (engineered).
Compared structures
- 5I2H · Crystal structure of O-methyltransferase family 2 protein Plim_1147 from Planctomyces… · 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 D5STZ7
- Elsewhere: RCSB PDB 5I2H · PDBe 5I2H · UniProt D5STZ7
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