MolNFT v1 · #54696 · protein
Structure of the N90S mutant of nitrite reductase from alcaligenes xylosoxidans complexed with nitrite
2XX1 · Dissimilatory copper-containing nitrite reductase: “Structure of the N90S mutant of nitrite reductase from alcaligenes xylosoxidans complexed with nitrite”. X-ray diffraction, 3 ligands (CU, SO4, NO2), 20 pockets (best druggability…
- 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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