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Structure of the N90S mutant of nitrite reductase from alcaligenes xylosoxidans complexed with nitrite
Analyse Structure of the N90S mutant of nitrite reductase from alcaligenes xylosoxidans… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2XX1
- Type
- protein
- Length
- 2,009 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dissimilatory copper-containing nitrite reductase
- EC
- 1.7.2.1
- UniProt
- O68601
- Ligands
- CU, SO4, NO2
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 10% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, E, F | Dissimilatory copper-containing nitrite reductase (EC 1.7.2.1) | protein | 335 | 10% helix, 42% strand | O68601 |
| C | Dissimilatory copper-containing nitrite reductase (EC 1.7.2.1) | protein | 334 | 10% helix, 43% strand | O68601 |
Ligands and binding sites
- CU · Copper (II) ion · metal · 12 copies · chains A, E, B, F, C, D
- SO4 · Sulfate ion · ion · 21 copies · chains A, E, B, C, D, F
- NO2 · Nitrite ion · ion · 6 copies · chains A, D, B, C, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 285 | 0.84 | 0.95 | 30 | SO4 |
| 2 | 282 | 0.84 | 0.95 | 29 | SO4 |
| 3 | 326 | 0.73 | 0.86 | 54 | empty |
| 4 | 715 | 0.73 | 0.79 | 72 | NO2 |
| 5 | 294 | 0.73 | 0.86 | 46 | empty |
Interfaces
9 interfaces between chains.
- B–C · 2367 Ų buried · 42 hydrogen bonds · protein-protein
- B–F · 2359 Ų buried · 43 hydrogen bonds · protein-protein
- A–D · 2336 Ų buried · 43 hydrogen bonds · protein-protein
- D–E · 2330 Ų buried · 44 hydrogen bonds · protein-protein
- A–E · 2302 Ų buried · 43 hydrogen bonds · protein-protein
Compared structures
- 2XX1 · STRUCTURE OF THE N90S MUTANT OF NITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS complexed… · 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 O68601
- Elsewhere: RCSB PDB 2XX1 · PDBe 2XX1 · UniProt O68601
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