Research workbench
Crystal structure of nitrite bound synthetic core domain of nitrite reductase from ralstonia pickettii (residues 1-331)
Analyse Crystal structure of nitrite bound 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
- 6QPT
- Type
- protein
- Length
- 1,918 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, NO2
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 9% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | 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, 47% strand | U3G913 |
| C, E | Copper-containing nitrite reductase (EC 1.7.2.1) | protein | 320 | 9% helix, 46% strand | U3G913 |
Ligands and binding sites
- CU · Copper (II) ion · metal · 12 copies · chains A, B, C, D, E, F
- NO2 · Nitrite ion · ion · 4 copies · chains B, C, A, D, E, F
- PG4 · Tetraethylene glycol · additive · 2 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1185 | 0.82 | 0.83 | 111 | NO2 |
| 2 | 396 | 0.81 | 0.90 | 44 | empty |
| 3 | 416 | 0.81 | 0.89 | 46 | empty |
| 4 | 50 | 0.70 | 0.98 | 12 | empty |
| 5 | 365 | 0.58 | 0.75 | 45 | empty |
Interfaces
9 interfaces between chains.
- E–F · 2317 Ų buried · 49 hydrogen bonds · protein-protein
- D–F · 2291 Ų buried · 50 hydrogen bonds · protein-protein
- D–E · 2288 Ų buried · 49 hydrogen bonds · protein-protein
- A–C · 2284 Ų buried · 47 hydrogen bonds · protein-protein
- B–C · 2269 Ų buried · 50 hydrogen bonds · protein-protein
Compared structures
- 6QPT · Crystal structure of nitrite bound 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 6QPT · PDBe 6QPT · UniProt U3G913
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