Research workbench
Methionine sulfoxide reductase a of corynebacterium diphtheriae
Analyse Methionine sulfoxide reductase a of corynebacterium diphtheriae in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4D7L
- Type
- protein
- Length
- 638 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptide methionine sulfoxide reductase msra
- UniProt
- Q6NEL2
- Ligands
- SO4
- Pockets
- 6 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Peptide methionine sulfoxide reductase msra | protein | 213 | 29% helix, 17% strand | Q6NEL2 |
| B | Peptide methionine sulfoxide reductase msra | protein | 212 | 28% helix, 17% strand | Q6NEL2 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C
- PGE · Triethylene glycol · additive · 19 copies · chains A, B, C
- CAC · Cacodylate ion · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 605 | 0.64 | 0.75 | 63 | PGE |
| 2 | 122 | 0.42 | 0.76 | 21 | empty |
| 3 | 99 | 0.35 | 0.74 | 24 | empty |
| 4 | 83 | 0.35 | 0.75 | 21 | SO4 |
| 5 | 87 | 0.33 | 0.73 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–C · 330 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 301 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 186 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4D7L · Methionine sulfoxide reductase A of Corynebacterium diphtheriae · the same entry in another collection · chain A against A, TM-score 1.00
- Q6NEL2 · AlphaFold monomer V2.0 prediction for peptide methionine sulfoxide reductase msra (Q6NEL2) · a predicted model of the same protein · chain A against A, TM-score 0.93
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 Q6NEL2
- Elsewhere: RCSB PDB 4D7L · PDBe 4D7L · UniProt Q6NEL2
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