Research workbench
Crystal structure of C-terminal despentapeptide nitrite reductase from achromobacter cycloclastes at PH5.0
Analyse Crystal structure of C-terminal despentapeptide nitrite reductase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1RZQ
- Type
- protein
- Length
- 988 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
- P25006
- Ligands
- CU, SO4
- Pockets
- 19 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 9% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Copper-containing nitrite reductase (EC 1.7.2.1) | protein | 328 | 9% helix, 42% strand | P25006 |
| C | Copper-containing nitrite reductase (EC 1.7.2.1) | protein | 332 | 9% helix, 42% strand | P25006 |
Ligands and binding sites
- CU · Copper (II) ion · metal · 6 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 5 copies · chains A, B, C
- ACY · Acetic acid · additive · 4 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 270 | 0.83 | 0.95 | 32 | empty |
| 2 | 497 | 0.81 | 0.88 | 51 | empty |
| 3 | 111 | 0.78 | 0.97 | 21 | empty |
| 4 | 124 | 0.77 | 0.96 | 22 | empty |
| 5 | 114 | 0.76 | 0.96 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1928 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 1880 Ų buried · 28 hydrogen bonds · protein-protein
- B–C · 1868 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 1RZQ · Crystal Structure of C-Terminal Despentapeptide Nitrite Reductase from Achromobacter… · the same entry in another collection · chain A against A, TM-score 1.00
- P25006 · AlphaFold monomer V2.0 prediction for copper-containing nitrite reductase (P25006) · a predicted model of the same protein · 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 P25006
- Elsewhere: RCSB PDB 1RZQ · PDBe 1RZQ · UniProt P25006
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