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Crystal structure of thiol-disulfide oxidoreductase from bacillus str. 'ames ancestor'
Analyse Crystal structure of thiol-disulfide oxidoreductase from bacillus str. 'ames… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NMU
- Type
- protein
- Length
- 573 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thiol-disulfide oxidoreductase resa
- UniProt
- Q81SZ9
- Ligands
- MG
- Pockets
- 4 · best druggability 0.64
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Thiol-disulfide oxidoreductase resa | protein | 147 | 39% helix, 26% strand | Q81SZ9 |
| B | Thiol-disulfide oxidoreductase resa | protein | 140 | 36% helix, 26% strand | Q81SZ9 |
| D | Thiol-disulfide oxidoreductase resa | protein | 139 | 37% helix, 27% strand | Q81SZ9 |
Ligands and binding sites
- MG · Magnesium ion · metal · chains D
- EDO · 1,2-ethanediol · additive · 15 copies · chains A, B, C, D
- ACY · Acetic acid · additive · 5 copies · chains A, B, D
- GOL · Glycerol · additive · 2 copies · chains A, B, C
- PEG · Di(hydroxyethyl)ether · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 648 | 0.64 | 0.74 | 66 | empty |
| 2 | 322 | 0.60 | 0.78 | 39 | empty |
| 3 | 288 | 0.56 | 0.76 | 30 | EDO |
| 4 | 168 | 0.54 | 0.80 | 35 | ACY, GOL, EDO |
Interfaces
5 interfaces between chains.
- A–B · 421 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 399 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 308 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 159 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 21 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified, 2 disulfide (engineered, disulfide).
Compared structures
- 4NMU · Crystal Structure of Thiol-disulfide Oxidoreductase from Bacillus str. 'Ames Ancestor' · the same entry in another collection · chain A against A, TM-score 1.00
- Q81SZ9 · AlphaFold monomer V2.0 prediction for thiol-disulfide oxidoreductase resa (Q81SZ9) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q81SZ9
- Elsewhere: RCSB PDB 4NMU · PDBe 4NMU · UniProt Q81SZ9
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