Research workbench
M144L mutant of nitrite reductase from alcaligenes xylosoxidans in space group P212121
Analyse M144L mutant of nitrite reductase from alcaligenes xylosoxidans in space group… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2JFC
- Type
- protein
- Length
- 2,010 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, CL
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 10% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Dissimilatory copper-containing nitrite reductase (EC 1.7.2.1) | protein | 335 | 10% helix, 43% strand | O68601 |
Ligands and binding sites
- CU · Copper (II) ion · metal · 12 copies · chains A, E, B, F, C, D
- CL · Chloride ion · ion · 4 copies · chains A, B, C, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 318 | 0.84 | 0.95 | 31 | empty |
| 2 | 320 | 0.84 | 0.95 | 33 | empty |
| 3 | 350 | 0.77 | 0.88 | 49 | empty |
| 4 | 347 | 0.76 | 0.87 | 51 | empty |
| 5 | 748 | 0.74 | 0.79 | 95 | empty |
Interfaces
9 interfaces between chains.
- A–D · 2287 Ų buried · 41 hydrogen bonds · protein-protein
- B–C · 2287 Ų buried · 38 hydrogen bonds · protein-protein
- B–F · 2284 Ų buried · 40 hydrogen bonds · protein-protein
- D–E · 2276 Ų buried · 39 hydrogen bonds · protein-protein
- A–E · 2275 Ų buried · 40 hydrogen bonds · protein-protein
Compared structures
- 2JFC · M144L mutant of Nitrite Reductase from Alcaligenes xylosoxidans in space group P212121 · 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 2JFC · PDBe 2JFC · UniProt O68601
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