Research workbench
Dhpi-SAM complex
Analyse Dhpi-SAM complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3OU6
- Type
- protein
- Length
- 845 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SAM-dependent methyltransferase
- UniProt
- D7PC21
- Ligands
- SAM, SO4
- Pockets
- 13 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | SAM-dependent methyltransferase | protein | 213 | 37% helix, 28% strand | D7PC21 |
| B | SAM-dependent methyltransferase | protein | 211 | 38% helix, 28% strand | D7PC21 |
| C | SAM-dependent methyltransferase | protein | 208 | 38% helix, 28% strand | D7PC21 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 178 | 0.79 | 0.94 | 37 | SAM, SO4 |
| 2 | 230 | 0.77 | 0.91 | 44 | SAM, SO4 |
| 3 | 332 | 0.76 | 0.87 | 54 | SAM, SO4 |
| 4 | 205 | 0.76 | 0.91 | 40 | SAM, SO4 |
| 5 | 613 | 0.75 | 0.82 | 76 | empty |
Interfaces
5 interfaces between chains.
- A–D · 1363 Ų buried · 27 hydrogen bonds · protein-protein
- B–C · 1352 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 689 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 670 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 183 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3OU6 · DhpI-SAM complex · 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 D7PC21
- Elsewhere: RCSB PDB 3OU6 · PDBe 3OU6 · UniProt D7PC21
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