MolNFT v1 · #184780 · protein
Green-type copper-nitrite reductase from sinorhizobium meliloti 2011
7P2F · Copper-containing nitrite reductase: “Green-type copper-nitrite reductase from sinorhizobium meliloti 2011”. X-ray diffraction, 1 ligand (CU), 12 pockets (best druggability 0.80). MolNFT v1 #184780 on GenesisL1: 3D structure…
- PDB
- 7P2F
- Type
- protein
- Length
- 985 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
- Q5SEZ8
- Ligands
- CU
- Pockets
- 12 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 9% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Copper-containing nitrite reductase (EC 1.7.2.1) | protein | 329 | 10% helix, 42% strand | Q5SEZ8 |
| B | Copper-containing nitrite reductase (EC 1.7.2.1) | protein | 328 | 9% helix, 41% strand | Q5SEZ8 |
| C | Copper-containing nitrite reductase (EC 1.7.2.1) | protein | 328 | 9% helix, 43% strand | Q5SEZ8 |
Ligands and binding sites
- CU · Copper (II) ion · metal · 6 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 357 | 0.80 | 0.90 | 35 | empty |
| 2 | 621 | 0.79 | 0.85 | 63 | empty |
| 3 | 60 | 0.73 | 0.99 | 18 | empty |
| 4 | 59 | 0.70 | 0.97 | 17 | empty |
| 5 | 90 | 0.49 | 0.82 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2151 Ų buried · 38 hydrogen bonds · protein-protein
- A–C · 2140 Ų buried · 34 hydrogen bonds · protein-protein
- B–C · 2100 Ų buried · 32 hydrogen bonds · protein-protein
Compared structures
- 7P2F · Green-type copper-nitrite reductase from Sinorhizobium meliloti 2011 · 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 Q5SEZ8
- Elsewhere: RCSB PDB 7P2F · PDBe 7P2F · UniProt Q5SEZ8
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