MolNFT v1 · #37994 · protein
Crystal structure of the FAD-containing pas domain of the protein nifl from azotobacter vinelandii.
2GJ3 · Nitrogen fixation regulatory protein: “Crystal structure of the FAD-containing pas domain of the protein nifl from azotobacter vinelandii.”. X-ray diffraction, 2 ligands (FAD, SO4), 4 pockets (best druggability 0.70). MolNFT v1…
- PDB
- 2GJ3
- Type
- protein
- Length
- 238 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nitrogen fixation regulatory protein
- EC
- 2.7.13.3
- UniProt
- P30663
- Ligands
- FAD, SO4
- Pockets
- 4 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nitrogen fixation regulatory protein (EC 2.7.13.3) | protein | 119 | 31% helix, 34% strand | P30663 |
| B | Nitrogen fixation regulatory protein (EC 2.7.13.3) | protein | 119 | 27% helix, 35% strand | P30663 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- EOH · Ethanol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 138 | 0.70 | 0.90 | 22 | FAD |
| 2 | 131 | 0.68 | 0.89 | 22 | FAD |
| 3 | 197 | 0.44 | 0.74 | 35 | empty |
| 4 | 66 | 0.35 | 0.77 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1044 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 2GJ3 · Crystal structure of the FAD-containing PAS domain of the protein NifL from Azotobacter… · the same entry in another collection · chain B against B, TM-score 1.00
- P30663 · AlphaFold monomer V2.0 prediction for nitrogen fixation regulatory protein (P30663) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 P30663
- Elsewhere: RCSB PDB 2GJ3 · PDBe 2GJ3 · UniProt P30663
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