Research workbench
Crystal structure of nitrite and no bound three-domain copper- containing nitrite reductase from hyphomicrobium denitrificans strain 1NES1
Analyse Crystal structure of nitrite and no bound three-domain copper- containing… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TFD
- Type
- protein
- Length
- 1,269 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Copper-containing nitrite reductase
- EC
- 1.7.2.1
- UniProt
- N0B9M5
- Ligands
- CU, NO2, NO
- Pockets
- 9 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 9% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Copper-containing nitrite reductase (EC 1.7.2.1) | protein | 423 | 9% helix, 46% strand | N0B9M5 |
Ligands and binding sites
- CU · Copper (II) ion · metal · 9 copies · chains A, C, B
- NO2 · Nitrite ion · ion · 2 copies · chains A, C, B
- NO · Nitric oxide · ion · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 602 | 0.86 | 0.91 | 89 | empty |
| 2 | 543 | 0.80 | 0.86 | 65 | NO |
| 3 | 613 | 0.79 | 0.85 | 67 | empty |
| 4 | 384 | 0.77 | 0.87 | 56 | empty |
| 5 | 154 | 0.59 | 0.83 | 22 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2468 Ų buried · 40 hydrogen bonds · protein-protein
- B–C · 2454 Ų buried · 42 hydrogen bonds · protein-protein
- A–C · 2426 Ų buried · 41 hydrogen bonds · protein-protein
Compared structures
- 6TFD · Crystal structure of nitrite and NO bound three-domain copper-containing nitrite… · 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 N0B9M5
- Elsewhere: RCSB PDB 6TFD · PDBe 6TFD · UniProt N0B9M5
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