Research workbench
High-resolution nitrite complex of a copper nitrite reductase determined by synchrotron radiation crystallography
Analyse High-resolution nitrite complex of a copper nitrite reductase determined by… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5D4H
- Type
- protein
- Length
- 1,017 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
- CU, NO2
- Pockets
- 13 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 12% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Copper-containing nitrite reductase (EC 1.7.2.1) | protein | 337 | 11% helix, 41% strand | P38501 |
| B | Copper-containing nitrite reductase (EC 1.7.2.1) | protein | 341 | 12% helix, 41% strand | P38501 |
| C | Copper-containing nitrite reductase (EC 1.7.2.1) | protein | 339 | 12% helix, 42% strand | P38501 |
Ligands and binding sites
- CU · Copper (II) ion · metal · 6 copies · chains A, C, B
- NO2 · Nitrite ion · ion · 3 copies · chains A, C, B
- GOL · Glycerol · additive · 22 copies · chains A, B, C
- ACY · Acetic acid · additive · 2 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 266 | 0.84 | 0.96 | 26 | GOL |
| 2 | 545 | 0.80 | 0.86 | 60 | empty |
| 3 | 68 | 0.76 | 0.99 | 17 | empty |
| 4 | 66 | 0.75 | 0.99 | 18 | empty |
| 5 | 60 | 0.73 | 0.98 | 18 | GOL |
Interfaces
3 interfaces between chains.
- B–C · 2304 Ų buried · 38 hydrogen bonds · protein-protein
- A–B · 2164 Ų buried · 38 hydrogen bonds · protein-protein
- A–C · 2098 Ų buried · 40 hydrogen bonds · protein-protein
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 5D4H · PDBe 5D4H · UniProt P38501
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