Research workbench
Precursor bound nifen
Analyse Precursor bound nifen in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PDI
- Type
- protein
- Length
- 3,436 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nitrogenase mofe cofactor biosynthesis protein nife; Nitrogenase mofe cofactor…
- UniProt
- C1DH03, C1DH04
- Ligands
- SF4, CZL
- Pockets
- 20 · best druggability 0.90
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | Nitrogenase mofe cofactor biosynthesis protein nife | protein | 427 | 47% helix, 14% strand | C1DH03 |
| B, D, F, H | Nitrogenase mofe cofactor biosynthesis protein nifn | protein | 432 | 44% helix, 15% strand | C1DH04 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 4 copies · chains A, B, C, D, E, F, G, H
- CZL · L-Cluster (Fe8S9) · ligand · 4 copies · chains A, C, E, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1044 | 0.90 | 0.92 | 132 | empty |
| 2 | 1021 | 0.90 | 0.92 | 141 | empty |
| 3 | 1053 | 0.90 | 0.91 | 131 | empty |
| 4 | 894 | 0.89 | 0.92 | 127 | empty |
| 5 | 1142 | 0.83 | 0.84 | 73 | empty |
Interfaces
12 interfaces between chains.
- E–F · 2658 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 2654 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 2639 Ų buried · 24 hydrogen bonds · protein-protein
- G–H · 2613 Ų buried · 24 hydrogen bonds · protein-protein
- B–D · 1321 Ų buried · 34 hydrogen bonds · protein-protein
Compared structures
- 3PDI · Precursor bound NifEN · 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 C1DH03
- Every structure of UniProt C1DH04
- Elsewhere: RCSB PDB 3PDI · PDBe 3PDI · UniProt C1DH03 · UniProt C1DH04
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