MolNFT v1 · #48315 · protein
Reduced H145A mutant of afnir exposed to no
2PPE · Copper-containing nitrite reductase: “Reduced H145A mutant of afnir exposed to no”. X-ray diffraction, 3 ligands (CU1, CU, NO), 11 pockets (best druggability 0.84). MolNFT v1 #48315 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2PPE
- 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
- 11 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 12% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Copper-containing nitrite reductase (EC 1.7.2.1) | protein | 336 | 13% helix, 42% strand | P38501 |
| B | Copper-containing nitrite reductase (EC 1.7.2.1) | protein | 337 | 12% helix, 43% strand | P38501 |
Ligands and binding sites
- CU1 · Copper (I) ion · metal · 3 copies · chains A, B, C
- CU · Copper (II) ion · metal · 3 copies · chains A, B, C
- NO · Nitric oxide · ion · chains B, C
- ACT · Acetate ion · additive · 2 copies · chains 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
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 259 | 0.84 | 0.96 | 30 | TRS |
| 2 | 572 | 0.80 | 0.86 | 61 | empty |
| 3 | 68 | 0.73 | 0.98 | 17 | empty |
| 4 | 62 | 0.72 | 0.98 | 17 | empty |
| 5 | 56 | 0.71 | 0.98 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2174 Ų buried · 36 hydrogen bonds · protein-protein
- A–C · 2119 Ų buried · 35 hydrogen bonds · protein-protein
- B–C · 2111 Ų buried · 38 hydrogen bonds · protein-protein
Compared structures
- 2PPE · Reduced H145A mutant of AfNiR exposed to NO · 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 2PPE · PDBe 2PPE · UniProt P38501
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