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Reduced crystal structure of the nitrosomonas europaea copper nitrite reductase at pH 6.5
Analyse Reduced crystal structure of the nitrosomonas europaea copper nitrite reductase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KNS
- Type
- protein
- Length
- 1,710 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Multicopper oxidase type 1
- UniProt
- Q82VX5
- Ligands
- CU, CL
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 8% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Multicopper oxidase type 1 | protein | 285 | 8% helix, 44% strand | Q82VX5 |
Ligands and binding sites
- CU · Copper (II) ion · metal · 12 copies · chains A, F, B, C, E, D
- CL · Chloride ion · ion · 4 copies · chains B, C, E
- GOL · Glycerol · additive · 2 copies · chains A, B, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 195 | 0.81 | 0.95 | 29 | empty |
| 2 | 183 | 0.81 | 0.95 | 22 | empty |
| 3 | 415 | 0.75 | 0.85 | 51 | empty |
| 4 | 399 | 0.75 | 0.85 | 47 | GOL |
| 5 | 595 | 0.68 | 0.77 | 59 | empty |
Interfaces
8 interfaces between chains.
- A–B · 1417 Ų buried · 20 hydrogen bonds · protein-protein
- B–F · 1412 Ų buried · 22 hydrogen bonds · protein-protein
- D–E · 1409 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 1405 Ų buried · 21 hydrogen bonds · protein-protein
- A–F · 1403 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 4KNS · Reduced crystal structure of the Nitrosomonas europaea copper nitrite reductase at pH 6.5 · the same entry in another collection · 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 Q82VX5
- Elsewhere: RCSB PDB 4KNS · PDBe 4KNS · UniProt Q82VX5
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