Research workbench
Reduced mutant D98N of afnir exposed to nitric oxide
Analyse Reduced mutant D98N of afnir exposed to nitric oxide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2PPF
- Type
- protein
- Length
- 1,009 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
- P38501
- Ligands
- CU1, CU, NO
- Pockets
- 13 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 11% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Copper-containing nitrite reductase (EC 1.7.2.1) | protein | 336 | 11% helix, 43% strand | P38501 |
| B | Copper-containing nitrite reductase (EC 1.7.2.1) | protein | 337 | 11% helix, 41% strand | P38501 |
Ligands and binding sites
- CU1 · Copper (I) ion · metal · 5 copies · chains A, B, C
- CU · Copper (II) ion · metal · 3 copies · chains A, B, C
- NO · Nitric oxide · ion · 4 copies · chains A, C, B
- ACT · Acetate ion · additive · 8 copies · chains A, B, C
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 274 | 0.85 | 0.96 | 29 | TRS |
| 2 | 564 | 0.81 | 0.86 | 66 | ACT |
| 3 | 68 | 0.74 | 0.98 | 17 | empty |
| 4 | 64 | 0.72 | 0.97 | 18 | empty |
| 5 | 56 | 0.70 | 0.97 | 16 | ACT |
Interfaces
3 interfaces between chains.
- A–B · 2160 Ų buried · 39 hydrogen bonds · protein-protein
- B–C · 2104 Ų buried · 40 hydrogen bonds · protein-protein
- A–C · 2089 Ų buried · 36 hydrogen bonds · protein-protein
Compared structures
- 2PPF · Reduced mutant D98N of AfNiR exposed to nitric oxide · 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 P38501
- Elsewhere: RCSB PDB 2PPF · PDBe 2PPF · UniProt P38501
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