Research workbench
Crystal structure of N-methyltransferase nods from bradyrhizobium japonicum WM9 in complex with S-adenosyl-L-homocysteine (sah)
Analyse Crystal structure of N-methyltransferase nods from bradyrhizobium japonicum WM9… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3OFK
- Type
- protein
- Length
- 783 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nodulation protein S
- EC
- 2.1.1.-
- UniProt
- Q9AQ22
- Ligands
- SAH
- Pockets
- 8 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nodulation protein S (EC 2.1.1.-) | protein | 204 | 38% helix, 27% strand | Q9AQ22 |
| B | Nodulation protein S (EC 2.1.1.-) | protein | 196 | 40% helix, 26% strand | Q9AQ22 |
| C | Nodulation protein S (EC 2.1.1.-) | protein | 202 | 41% helix, 25% strand | Q9AQ22 |
| D | Nodulation protein S (EC 2.1.1.-) | protein | 181 | 37% helix, 31% strand | Q9AQ22 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 220 | 0.77 | 0.91 | 46 | SAH |
| 2 | 543 | 0.76 | 0.83 | 63 | SAH |
| 3 | 314 | 0.76 | 0.87 | 50 | SAH |
| 4 | 437 | 0.69 | 0.81 | 47 | empty |
| 5 | 336 | 0.61 | 0.78 | 57 | empty |
Interfaces
5 interfaces between chains.
- B–C · 944 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 717 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 514 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 174 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 13 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3OFK · Crystal structure of N-methyltransferase NodS from Bradyrhizobium japonicum WM9 in… · 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 Q9AQ22
- Elsewhere: RCSB PDB 3OFK · PDBe 3OFK · UniProt Q9AQ22
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