Research workbench
X-ray crystal structure of an O-methyltransferase from anaplasma phagocytophilum bound to sah solved by iodide sad phasing
Analyse X-ray crystal structure of an O-methyltransferase from anaplasma… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4OA5
- Type
- protein
- Length
- 1,276 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- O-methyltransferase family protein
- EC
- 2.1.1.-
- UniProt
- Q2GKC7
- Ligands
- SAH, IOD
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | O-methyltransferase family protein (EC 2.1.1.-) | protein | 212 | 48% helix, 20% strand | Q2GKC7 |
| D, F | O-methyltransferase family protein (EC 2.1.1.-) | protein | 213 | 47% helix, 20% strand | Q2GKC7 |
| E | O-methyltransferase family protein (EC 2.1.1.-) | protein | 214 | 47% helix, 20% strand | Q2GKC7 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 6 copies · chains A, B, C, D, E, F
- IOD · Iodide ion · ion · 114 copies · chains A, F, D, B, C, E
- EDO · 1,2-ethanediol · additive · 10 copies · chains A, D, F, B, C, E
- GOL · Glycerol · additive · 4 copies · chains A, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 707 | 0.73 | 0.79 | 75 | IOD |
| 2 | 58 | 0.72 | 0.98 | 18 | IOD |
| 3 | 121 | 0.65 | 0.88 | 29 | IOD |
| 4 | 526 | 0.61 | 0.74 | 46 | IOD, EDO |
| 5 | 274 | 0.59 | 0.79 | 46 | SAH, IOD |
Interfaces
8 interfaces between chains.
- A–F · 1801 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 1770 Ų buried · 9 hydrogen bonds · protein-protein
- C–E · 745 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 670 Ų buried · 5 hydrogen bonds · protein-protein
- D–E · 663 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4OA5 · X-ray crystal structure of an O-methyltransferase from Anaplasma phagocytophilum bound to… · the same entry in another collection · chain F against F, 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 Q2GKC7
- Elsewhere: RCSB PDB 4OA5 · PDBe 4OA5 · UniProt Q2GKC7
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