MolNFT v1 · #77786 · protein
The structure of a B12-independent methionine synthase from shewanella sp. W3-18-1 in complex with selenomethionine.
3RPD · Methionine synthase (B12-independent): “The structure of a B12-independent methionine synthase from shewanella sp. W3-18-1 in complex with…”. X-ray diffraction, 2 ligands (MSE, ZN), 7 pockets (best druggability 0.71). MolNFT v1…
- PDB
- 3RPD
- Type
- protein
- Length
- 686 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methionine synthase (B12-independent)
- EC
- 2.1.1.14
- UniProt
- A1RHE8
- Ligands
- MSE, ZN
- Pockets
- 7 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methionine synthase (B12-independent) (EC 2.1.1.14) | protein | 345 | 41% helix, 18% strand | A1RHE8 |
| B | Methionine synthase (B12-independent) (EC 2.1.1.14) | protein | 341 | 42% helix, 18% strand | A1RHE8 |
Ligands and binding sites
- MSE · Selenomethionine · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 83 | 0.71 | 0.95 | 30 | MSE |
| 2 | 56 | 0.69 | 0.97 | 24 | ZN, MSE |
| 3 | 276 | 0.62 | 0.80 | 42 | empty |
| 4 | 277 | 0.59 | 0.79 | 37 | empty |
| 5 | 91 | 0.36 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 726 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 modified (engineered).
Compared structures
- 3RPD · The structure of a B12-independent methionine synthase from Shewanella sp. W3-18-1 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 A1RHE8
- Elsewhere: RCSB PDB 3RPD · PDBe 3RPD · UniProt A1RHE8
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.