Research workbench
Crystal structure of NIF3 superfamily protein from sphaerobacter thermophilus
Analyse Crystal structure of NIF3 superfamily protein from sphaerobacter thermophilus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3RXY
- Type
- protein
- Length
- 1,652 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NIF3 protein
- UniProt
- D1C210
- Ligands
- CL
- Pockets
- 18 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | NIF3 protein | protein | 276 | 53% helix, 14% strand | D1C210 |
| C, D, E, F | NIF3 protein | protein | 275 | 52% helix, 14% strand | D1C210 |
Ligands and binding sites
- CL · Chloride ion · ion · 7 copies · chains A, B, C, D, E, F
- FMT · Formic acid · additive · 14 copies · chains A, B, C, D, E, F
- ACT · Acetate ion · additive · chains E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 969 | 0.70 | 0.75 | 121 | FMT, CL, ACT |
| 2 | 790 | 0.68 | 0.75 | 108 | FMT, CL |
| 3 | 478 | 0.62 | 0.75 | 32 | empty |
| 4 | 527 | 0.62 | 0.75 | 47 | empty |
| 5 | 366 | 0.58 | 0.76 | 46 | FMT, CL |
Interfaces
8 interfaces between chains.
- B–D · 986 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 976 Ų buried · 11 hydrogen bonds · protein-protein
- A–E · 976 Ų buried · 8 hydrogen bonds · protein-protein
- E–F · 974 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 961 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 66 modified (engineered).
Compared structures
- 3RXY · Crystal structure of NIF3 superfamily protein from Sphaerobacter thermophilus · 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 D1C210
- Elsewhere: RCSB PDB 3RXY · PDBe 3RXY · UniProt D1C210
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