Research workbench
Solution structure of the complex between nitrite reductase and pseudoazurin from a. faecalis
Analyse Solution structure of the complex between nitrite reductase and pseudoazurin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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