MolNFT v1 · #174015 · protein
An unexpected P-cluster like intermediate en route to the nitrogenase femo-co
7BI7 · Femo cofactor biosynthesis protein nifb: “An unexpected P-cluster like intermediate en route to the nitrogenase femo-co”. X-ray diffraction, 4 ligands (SF4, CLF, H2S), 6 pockets (best druggability 0.87). MolNFT v1 #174015 on…
- PDB
- 7BI7
- Type
- protein
- Length
- 550 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Femo cofactor biosynthesis protein nifb
- UniProt
- O27899
- Ligands
- SF4, CLF, H2S, NO3
- Pockets
- 6 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Femo cofactor biosynthesis protein nifb | protein | 279 | 32% helix, 20% strand | O27899 |
| B | Femo cofactor biosynthesis protein nifb | protein | 271 | 34% helix, 21% strand | O27899 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 2 copies · chains A, B
- CLF · FE(8)-S(7) cluster · ligand · 2 copies · chains A, B
- H2S · Hydrosulfuric acid · ion · 2 copies · chains A, B
- NO3 · Nitrate ion · ion · chains A
- MLI · Malonate ion · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 422 | 0.87 | 0.95 | 50 | SF4, CLF, H2S, NO3 |
| 2 | 423 | 0.86 | 0.94 | 52 | SF4, CLF, H2S |
| 3 | 158 | 0.65 | 0.86 | 24 | empty |
| 4 | 203 | 0.61 | 0.82 | 38 | empty |
| 5 | 271 | 0.56 | 0.77 | 37 | empty |
Interfaces
1 interface between chains.
- A–B · 776 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 7BI7 · An Unexpected P-Cluster like Intermediate En Route to the Nitrogenase FeMo-co · 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 O27899
- Elsewhere: RCSB PDB 7BI7 · PDBe 7BI7 · UniProt O27899
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