Research workbench
High resolution synchrotron structure of copper nitrite reductase from alcaligenes faecalis
Analyse High resolution synchrotron structure of copper nitrite reductase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YSE
- Type
- protein
- Length
- 1,011 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
- Pockets
- 12 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 11% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Copper-containing nitrite reductase (EC 1.7.2.1) | protein | 337 | 11% helix, 41% strand | P38501 |
Ligands and binding sites
- CU · Copper (II) ion · metal · 6 copies · chains A, C, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 6 copies · chains A, B, C
- ACY · Acetic acid · additive · 5 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 268 | 0.84 | 0.96 | 28 | empty |
| 2 | 521 | 0.81 | 0.87 | 60 | empty |
| 3 | 60 | 0.74 | 0.99 | 17 | empty |
| 4 | 58 | 0.73 | 0.99 | 17 | empty |
| 5 | 161 | 0.49 | 0.77 | 42 | MPD, ACY |
Interfaces
3 interfaces between chains.
- A–B · 2185 Ų buried · 40 hydrogen bonds · protein-protein
- B–C · 2180 Ų buried · 38 hydrogen bonds · protein-protein
- A–C · 2164 Ų buried · 40 hydrogen bonds · protein-protein
Compared structures
- 4YSE · High resolution synchrotron structure of copper nitrite reductase from Alcaligenes… · 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 P38501
- Elsewhere: RCSB PDB 4YSE · PDBe 4YSE · UniProt P38501
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