Research workbench
Glycerol trinitrate reductase nera from agrobacterium radiobacter
Analyse Glycerol trinitrate reductase nera from agrobacterium radiobacter in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JIC
- Type
- protein
- Length
- 1,110 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gtn reductase
- UniProt
- O31246
- Ligands
- FMN, SO4
- Pockets
- 8 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Gtn reductase | protein | 370 | 35% helix, 15% strand | O31246 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 3 copies · chains A, B, C
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 482 | 0.69 | 0.80 | 69 | empty |
| 2 | 346 | 0.69 | 0.82 | 35 | FMN |
| 3 | 430 | 0.68 | 0.79 | 44 | FMN, PEG |
| 4 | 290 | 0.67 | 0.82 | 41 | FMN |
| 5 | 191 | 0.58 | 0.81 | 24 | empty |
Interfaces
3 interfaces between chains.
- A–B · 582 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 422 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 172 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4JIC · Glycerol Trinitrate Reductase NerA from Agrobacterium radiobacter · 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 O31246
- Elsewhere: RCSB PDB 4JIC · PDBe 4JIC · UniProt O31246
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