Research workbench
Mgadp-bound fe protein of the iron-only nitrogenase from azotobacter vinelandii
Analyse Mgadp-bound fe protein of the iron-only nitrogenase from azotobacter vinelandii in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7QQA
- Type
- protein
- Length
- 1,088 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nitrogenase iron protein
- EC
- 1.18.6.1
- UniProt
- C1DK95
- Ligands
- ADP, SF4, MG
- Pockets
- 7 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Nitrogenase iron protein (EC 1.18.6.1) | protein | 273 | 45% helix, 16% strand | C1DK95 |
| B, C | Nitrogenase iron protein (EC 1.18.6.1) | protein | 271 | 44% helix, 16% strand | C1DK95 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- SF4 · Iron/sulfur cluster · ligand · 2 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1010 | 0.84 | 0.84 | 114 | SF4 |
| 2 | 786 | 0.82 | 0.85 | 109 | ADP, MG |
| 3 | 1139 | 0.81 | 0.82 | 111 | ADP, MG |
| 4 | 294 | 0.70 | 0.85 | 41 | ADP, MG |
| 5 | 340 | 0.69 | 0.82 | 31 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1278 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 1237 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 676 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 462 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 176 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 7QQA · MgADP-bound Fe protein of the iron-only nitrogenase from Azotobacter vinelandii · 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 C1DK95
- Elsewhere: RCSB PDB 7QQA · PDBe 7QQA · UniProt C1DK95
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.