MolNFT v1 · #11004 · protein
Crystal structure of nitrite soaked reduced D98N afnir
1J9R · Copper-containing nitrite reductase: “Crystal structure of nitrite soaked reduced D98N afnir”. X-ray diffraction, 2 ligands (CU, NO2), 10 pockets (best druggability 0.84). MolNFT v1 #11004 on GenesisL1: 3D structure, binding sites…
- PDB
- 1J9R
- Type
- protein
- Length
- 1,008 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Copper-containing nitrite reductase
- EC
- 1.7.99.3
- UniProt
- P38501
- Ligands
- CU, NO2
- Pockets
- 10 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 11% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Copper-containing nitrite reductase (EC 1.7.99.3) | protein | 336 | 11% helix, 42% strand | P38501 |
Ligands and binding sites
- CU · Copper (II) ion · metal · 9 copies · chains A, B, C
- NO2 · Nitrite ion · ion · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 270 | 0.84 | 0.96 | 31 | empty |
| 2 | 572 | 0.80 | 0.86 | 67 | empty |
| 3 | 62 | 0.73 | 0.98 | 16 | empty |
| 4 | 62 | 0.72 | 0.98 | 17 | empty |
| 5 | 57 | 0.71 | 0.98 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–C · 2113 Ų buried · 34 hydrogen bonds · protein-protein
- B–C · 2104 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 2104 Ų buried · 37 hydrogen bonds · protein-protein
Compared structures
- 1J9R · Crystal structure of nitrite soaked reduced D98N AFNIR · the same entry in another collection · chain A against A, TM-score 1.00
- P38501 · AlphaFold monomer V2.0 prediction for copper-containing nitrite reductase (P38501) · 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 P38501
- Elsewhere: RCSB PDB 1J9R · PDBe 1J9R · UniProt P38501
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