Research workbench
Structure of the recombinant native nitrite reductase from alcaligenes xylosoxidans complexed with nitrite
Analyse Structure of the recombinant native nitrite reductase from alcaligenes… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2XWZ
- 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, NO
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 11% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Dissimilatory copper-containing nitrite reductase (EC 1.7.2.1) | protein | 335 | 11% helix, 42% strand | O68601 |
| F | Dissimilatory copper-containing nitrite reductase (EC 1.7.2.1) | protein | 334 | 11% 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 · 44 copies · chains A, D, B, C, F, E
- NO2 · Nitrite ion · ion · 4 copies · chains A, E, D, B, F, C
- NO · Nitric oxide · ion · 2 copies · chains B, C, D, E
- ACT · Acetate ion · additive · 11 copies · chains A, E, B, F, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 303 | 0.84 | 0.95 | 31 | empty |
| 2 | 304 | 0.84 | 0.95 | 32 | empty |
| 3 | 330 | 0.76 | 0.87 | 48 | empty |
| 4 | 294 | 0.76 | 0.88 | 50 | empty |
| 5 | 886 | 0.75 | 0.79 | 110 | ACT, NO, NO2 |
Interfaces
10 interfaces between chains.
- C–F · 2301 Ų buried · 42 hydrogen bonds · protein-protein
- A–D · 2292 Ų buried · 42 hydrogen bonds · protein-protein
- B–F · 2286 Ų buried · 44 hydrogen bonds · protein-protein
- D–E · 2285 Ų buried · 40 hydrogen bonds · protein-protein
- B–C · 2284 Ų buried · 42 hydrogen bonds · protein-protein
Compared structures
- 2XWZ · STRUCTURE OF THE RECOMBINANT NATIVE NITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS… · 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 2XWZ · PDBe 2XWZ · UniProt O68601
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