MolNFT v1 · #161272 · protein
Mgadp-bound fe protein of vanadium nitrogenase from azotobacter vinelandii
6Q93 · Nitrogenase iron protein: “Mgadp-bound fe protein of vanadium nitrogenase from azotobacter vinelandii”. X-ray diffraction, 3 ligands (ADP, SF4, MG), 19 pockets (best druggability 0.85). MolNFT v1 #161272 on GenesisL1: 3D structure…
- PDB
- 6Q93
- Type
- protein
- Length
- 2,213 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nitrogenase iron protein
- EC
- 1.18.6.1
- UniProt
- C1DI30
- Ligands
- ADP, SF4, MG
- Pockets
- 19 · best druggability 0.85
Structure
x-ray diffraction · 7 distinct chains · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nitrogenase iron protein (EC 1.18.6.1) | protein | 276 | 42% helix, 16% strand | C1DI30 |
| B | Nitrogenase iron protein (EC 1.18.6.1) | protein | 274 | 41% helix, 16% strand | C1DI30 |
| C | Nitrogenase iron protein (EC 1.18.6.1) | protein | 284 | 40% helix, 15% strand | C1DI30 |
| D, G | Nitrogenase iron protein (EC 1.18.6.1) | protein | 272 | 43% helix, 16% strand | C1DI30 |
| E | Nitrogenase iron protein (EC 1.18.6.1) | protein | 275 | 43% helix, 16% strand | C1DI30 |
| F | Nitrogenase iron protein (EC 1.18.6.1) | protein | 273 | 42% helix, 16% strand | C1DI30 |
| H | Nitrogenase iron protein (EC 1.18.6.1) | protein | 287 | 41% helix, 15% strand | C1DI30 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- SF4 · Iron/sulfur cluster · ligand · 4 copies · chains A, B, C, D, E, F, G, H
- MG · Magnesium ion · metal · 10 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 948 | 0.85 | 0.87 | 99 | ADP, MG |
| 2 | 676 | 0.81 | 0.86 | 78 | ADP, MG |
| 3 | 611 | 0.79 | 0.85 | 69 | ADP, MG |
| 4 | 556 | 0.77 | 0.84 | 54 | ADP, MG |
| 5 | 467 | 0.76 | 0.84 | 65 | ADP, MG |
Interfaces
19 interfaces between chains.
- G–H · 1757 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1721 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1543 Ų buried · 11 hydrogen bonds · protein-protein
- E–F · 1336 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 421 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6Q93 · MgADP-bound Fe protein of Vanadium 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 C1DI30
- Elsewhere: RCSB PDB 6Q93 · PDBe 6Q93 · UniProt C1DI30
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.