MolNFT v1 · #31602 · protein
Reduced acetamide-bound M150G nitrite reductase from alcaligenes faecalis
2B08 · Copper-containing nitrite reductase: “Reduced acetamide-bound M150G nitrite reductase from alcaligenes faecalis”. X-ray diffraction, 2 ligands (ACM, CU1), 12 pockets (best druggability 0.84). MolNFT v1 #31602 on GenesisL1: 3D…
- PDB
- 2B08
- Type
- protein
- Length
- 1,007 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
- ACM, CU1
- Pockets
- 12 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 13% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Copper-containing nitrite reductase (EC 1.7.2.1) | protein | 335 | 13% helix, 43% strand | P38501 |
| B, C | Copper-containing nitrite reductase (EC 1.7.2.1) | protein | 336 | 13% helix, 43% strand | P38501 |
Ligands and binding sites
- ACM · Acetamide · ligand · 4 copies · chains A, B, C
- CU1 · Copper (I) ion · metal · 9 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 255 | 0.84 | 0.96 | 30 | empty |
| 2 | 566 | 0.80 | 0.86 | 68 | empty |
| 3 | 55 | 0.71 | 0.98 | 16 | empty |
| 4 | 55 | 0.70 | 0.97 | 17 | empty |
| 5 | 53 | 0.69 | 0.97 | 16 | empty |
Interfaces
3 interfaces between chains.
- B–C · 2123 Ų buried · 39 hydrogen bonds · protein-protein
- A–C · 2118 Ų buried · 35 hydrogen bonds · protein-protein
- A–B · 2118 Ų buried · 36 hydrogen bonds · protein-protein
Compared structures
- 2B08 · Reduced acetamide-bound M150G Nitrite Reductase from Alcaligenes faecalis · 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 2B08 · PDBe 2B08 · UniProt P38501
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