Research workbench
Anaerobically manipulated wild type oxidized afnir bound to nitrous oxide
Analyse Anaerobically manipulated wild type oxidized afnir bound to nitrous oxide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2PPA
- 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, N2O
- Pockets
- 10 · best druggability 0.84
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 | 12% helix, 41% 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
- N2O · Nitrous oxide · ion · 2 copies · chains A, B, C
- ACT · Acetate ion · additive · 10 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
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 260 | 0.84 | 0.96 | 25 | TRS |
| 2 | 523 | 0.80 | 0.87 | 65 | ACT |
| 3 | 58 | 0.71 | 0.97 | 18 | empty |
| 4 | 53 | 0.70 | 0.97 | 17 | empty |
| 5 | 105 | 0.51 | 0.82 | 35 | CU, ACT, N2O |
Interfaces
3 interfaces between chains.
- A–B · 2159 Ų buried · 38 hydrogen bonds · protein-protein
- B–C · 2106 Ų buried · 42 hydrogen bonds · protein-protein
- A–C · 2100 Ų buried · 36 hydrogen bonds · protein-protein
Compared structures
- 2PPA · Anaerobically manipulated wild type oxidized AfNiR bound to nitrous oxide · the same entry in another collection · chain C against C, 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 2PPA · PDBe 2PPA · UniProt P38501
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