Research workbench
Bifunctional methionine sulfoxide reductase ab (msrab) from treponema denticola
Analyse Bifunctional methionine sulfoxide reductase ab (msrab) from treponema denticola in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FA9
- Type
- protein
- Length
- 607 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptide methionine sulfoxide reductase msra
- EC
- 1.8.4.11
- UniProt
- Q73PT7
- Ligands
- D1D
- Pockets
- 6 · best druggability 0.54
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptide methionine sulfoxide reductase msra (EC 1.8.4.11) | protein | 303 | 28% helix, 26% strand | Q73PT7 |
| B | Peptide methionine sulfoxide reductase msra (EC 1.8.4.11) | protein | 304 | 29% helix, 26% strand | Q73PT7 |
Ligands and binding sites
- D1D · (4S,5S)-1,2-dithiane-4,5-diol · ligand · 2 copies · chains A, B
- DTT · 2,3-dihydroxy-1,4-dithiobutane · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 185 | 0.54 | 0.79 | 26 | DTT |
| 2 | 219 | 0.54 | 0.78 | 27 | DTT |
| 3 | 223 | 0.54 | 0.77 | 27 | DTT |
| 4 | 240 | 0.53 | 0.76 | 36 | empty |
| 5 | 89 | 0.35 | 0.74 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 940 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 5FA9 · Bifunctional Methionine Sulfoxide Reductase AB (MsrAB) from Treponema denticola · 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 Q73PT7
- Elsewhere: RCSB PDB 5FA9 · PDBe 5FA9 · UniProt Q73PT7
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