Research workbench
X-ray structure of free methionine-R-sulfoxide reductase from neisseria meningitidis in complex with its substrate
Analyse X-ray structure of free methionine-R-sulfoxide reductase from neisseria… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MMH
- Type
- protein
- Length
- 334 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methionine-R-sulfoxide reductase
- EC
- 1.8.4.14
- UniProt
- C9X208
- Ligands
- SME, MG
- Pockets
- 3 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Methionine-R-sulfoxide reductase (EC 1.8.4.14) | protein | 167 | 41% helix, 25% strand | C9X208 |
Ligands and binding sites
- SME · Methionine sulfoxide · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 9 copies · chains A, B
- MRD · (4R)-2-methylpentane-2,4-diol · additive · 4 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 66 | 0.72 | 0.97 | 20 | SME |
| 2 | 59 | 0.70 | 0.97 | 20 | SME |
| 3 | 312 | 0.52 | 0.74 | 34 | empty |
Interfaces
1 interface between chains.
- A–B · 1190 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3MMH · X-ray structure of free methionine-R-sulfoxide reductase from neisseria meningitidis 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 C9X208
- Elsewhere: RCSB PDB 3MMH · PDBe 3MMH · UniProt C9X208
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