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Crystal structure of as isolated synthetic core domain of nitrite reductase from ralstonia pickettii (residues 1-331)
Analyse Crystal structure of as isolated synthetic core domain of nitrite reductase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6QPU
- Type
- protein
- Length
- 1,921 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Copper-containing nitrite reductase
- EC
- 1.7.2.1
- UniProt
- U3G913
- Ligands
- CU, CL
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 5 distinct chains · 9% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Copper-containing nitrite reductase (EC 1.7.2.1) | protein | 320 | 9% helix, 46% strand | U3G913 |
| B, D | Copper-containing nitrite reductase (EC 1.7.2.1) | protein | 319 | 9% helix, 46% strand | U3G913 |
| C | Copper-containing nitrite reductase (EC 1.7.2.1) | protein | 322 | 9% helix, 46% strand | U3G913 |
| E | Copper-containing nitrite reductase (EC 1.7.2.1) | protein | 320 | 9% helix, 46% strand | U3G913 |
| F | Copper-containing nitrite reductase (EC 1.7.2.1) | protein | 321 | 9% helix, 46% strand | U3G913 |
Ligands and binding sites
- CU · Copper (II) ion · metal · 12 copies · chains A, B, C, D, E, F
- CL · Chloride ion · ion · 6 copies · chains A, B, C, D, E, F
- PG4 · Tetraethylene glycol · additive · 3 copies · chains A, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1197 | 0.83 | 0.83 | 123 | CL |
| 2 | 361 | 0.82 | 0.92 | 38 | empty |
| 3 | 496 | 0.82 | 0.88 | 74 | empty |
| 4 | 88 | 0.54 | 0.85 | 26 | empty |
| 5 | 94 | 0.53 | 0.84 | 24 | empty |
Interfaces
10 interfaces between chains.
- D–F · 2340 Ų buried · 49 hydrogen bonds · protein-protein
- E–F · 2335 Ų buried · 49 hydrogen bonds · protein-protein
- A–C · 2310 Ų buried · 50 hydrogen bonds · protein-protein
- D–E · 2305 Ų buried · 49 hydrogen bonds · protein-protein
- B–C · 2302 Ų buried · 47 hydrogen bonds · protein-protein
Compared structures
- 6QPU · Crystal structure of as isolated synthetic core domain of nitrite reductase from… · 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 U3G913
- Elsewhere: RCSB PDB 6QPU · PDBe 6QPU · UniProt U3G913
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