MolNFT v1 · #47756 · protein
Solution structure of the complex between nitrite reductase and pseudoazurin from a. faecalis
2P80 · Copper-containing nitrite reductase: “Solution structure of the complex between nitrite reductase and pseudoazurin from a. faecalis”. Solution nmr, 2 ligands (GD, CU), 16 pockets (best druggability 0.84). MolNFT v1 #47756 on…
- PDB
- 2P80
- Type
- protein
- Length
- 1,130 residues
- Chains
- 4
- Method
- solution nmr
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Copper-containing nitrite reductase; Pseudoazurin
- EC
- 1.7.2.1
- UniProt
- P38501, P04377
- Ligands
- GD, CU
- Pockets
- 16 · best druggability 0.84
Structure
solution nmr · 3 distinct chains · 13% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Copper-containing nitrite reductase (EC 1.7.2.1) | protein | 335 | 12% helix, 39% strand | P38501 |
| B, C | Copper-containing nitrite reductase (EC 1.7.2.1) | protein | 336 | 12% helix, 40% strand | P38501 |
| D | Pseudoazurin | protein | 123 | 17% helix, 37% strand | P04377 |
Ligands and binding sites
- GD · Gadolinium atom · metal · 9 copies · chains A, B, C
- CU · Copper (II) ion · metal · 7 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 304 | 0.84 | 0.95 | 40 | empty |
| 2 | 522 | 0.80 | 0.87 | 58 | empty |
| 3 | 60 | 0.72 | 0.97 | 16 | empty |
| 4 | 737 | 0.72 | 0.78 | 76 | empty |
| 5 | 59 | 0.71 | 0.97 | 18 | empty |
Interfaces
5 interfaces between chains.
- B–C · 2083 Ų buried · 33 hydrogen bonds · protein-protein
- A–B · 2082 Ų buried · 32 hydrogen bonds · protein-protein
- A–C · 2069 Ų buried · 33 hydrogen bonds · protein-protein
- C–D · 699 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 104 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2P80 · Solution structure of the complex between nitrite reductase and pseudoazurin from A.… · 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
- P04377 · AlphaFold monomer V2.0 prediction for pseudoazurin (P04377) · a predicted model of the same protein · chain D against A, TM-score 0.98
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
- Every structure of UniProt P04377
- Elsewhere: RCSB PDB 2P80 · PDBe 2P80 · UniProt P38501 · UniProt P04377
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