Research workbench
Crystal structure of IscU D40A/H106A variant
Analyse Crystal structure of IscU D40A/H106A variant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7C8O
- Type
- protein
- Length
- 467 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.84
- Source
- Methanothrix thermoacetophila
- Molecule
- Nitrogen-fixing NifU domain protein
- UniProt
- A0B757
- Ligands
- FES
- Pockets
- 4 · best druggability 0.81
Structure
x-ray diffraction · resolution 1.84 · 4 distinct chains · 44% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nitrogen-fixing NifU domain protein | protein | 118 | 45% helix, 25% strand | A0B757 |
| B | Nitrogen-fixing NifU domain protein | protein | 117 | 44% helix, 22% strand | A0B757 |
| C | Nitrogen-fixing NifU domain protein | protein | 120 | 43% helix, 25% strand | A0B757 |
| D | Nitrogen-fixing NifU domain protein | protein | 112 | 44% helix, 23% strand | A0B757 |
Ligands and binding sites
- FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains A, D, B, C
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 | 494 | 0.81 | 0.88 | 81 | empty |
| 2 | 88 | 0.55 | 0.85 | 20 | empty |
| 3 | 119 | 0.43 | 0.77 | 19 | empty |
| 4 | 87 | 0.37 | 0.76 | 18 | empty |
Interfaces
5 interfaces between chains.
- B–D · 765 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 617 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 568 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 561 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 557 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 7C8O · Crystal structure of iscu D40A/H106A variant · 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 A0B757
- Elsewhere: RCSB PDB 7C8O · PDBe 7C8O · UniProt A0B757
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