Research workbench
Tpr domain of nrfg mediates the complex formation between heme lyase and formate-dependent nitrite reductase in escherichia COLI O157:H7
Analyse Tpr domain of nrfg mediates the complex formation between heme lyase and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2E2E
- Type
- protein
- Length
- 342 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Formate-dependent nitrite reductase complex nrfg subunit
- UniProt
- Q8X5S3
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 65% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Formate-dependent nitrite reductase complex nrfg subunit | protein | 171 | 65% helix, 0% strand | Q8X5S3 |
Ligands and binding sites
- BME · Beta-mercaptoethanol · additive · 2 copies · chains A, B
- IMD · Imidazole · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 516 | 0.74 | 0.82 | 49 | BME |
| 2 | 217 | 0.54 | 0.78 | 25 | empty |
| 3 | 254 | 0.53 | 0.76 | 26 | empty |
| 4 | 111 | 0.53 | 0.83 | 20 | empty |
| 5 | 72 | 0.38 | 0.79 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 621 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 2E2E · TPR domain of NrfG mediates the complex formation between heme lyase and… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8X5S3 · AlphaFold monomer V2.0 prediction for formate-dependent nitrite reductase complex subunit… · a predicted model of the same protein · chain A against A, TM-score 0.88
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 Q8X5S3
- Elsewhere: RCSB PDB 2E2E · PDBe 2E2E · UniProt Q8X5S3
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