MolNFT v1 · #30973 · protein
Structure of alcaligenes faecalis nitrite reductase and a copper site mutant, M150E, that contains zinc
2AFN: “Structure of alcaligenes faecalis nitrite reductase and a copper site mutant, M150E, that contains zinc”. X-ray diffraction, 1 ligand (CU), 12 pockets (best druggability 0.84). MolNFT v1 #30973 on GenesisL1: 3D structure, binding…
- PDB
- 2AFN
- Type
- protein
- Length
- 993 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nitrite reductase
- EC
- 1.7.99.3
- UniProt
- P38501
- Ligands
- CU
- Pockets
- 12 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 10% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Nitrite reductase (EC 1.7.99.3) | protein | 331 | 10% helix, 42% strand | P38501 |
Ligands and binding sites
- CU · Copper (II) ion · metal · 6 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 299 | 0.84 | 0.95 | 29 | empty |
| 2 | 541 | 0.80 | 0.86 | 58 | empty |
| 3 | 66 | 0.74 | 0.98 | 18 | empty |
| 4 | 62 | 0.71 | 0.97 | 18 | empty |
| 5 | 54 | 0.69 | 0.97 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2109 Ų buried · 33 hydrogen bonds · protein-protein
- A–C · 2089 Ų buried · 31 hydrogen bonds · protein-protein
- B–C · 2075 Ų buried · 34 hydrogen bonds · protein-protein
Compared structures
- 2AFN · Structure of alcaligenes faecalis nitrite reductase and a copper site mutant, M150E, that… · 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 2AFN · PDBe 2AFN · UniProt P38501
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