Research workbench
Crystallographic structure of a blue copper nitrite reductase from alcaligenes xylosoxidans
Analyse Crystallographic structure of a blue copper nitrite reductase from alcaligenes… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1NDR
- Type
- protein
- Length
- 990 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nitrite reductase
- EC
- 1.7.99.3
- UniProt
- P81445
- Ligands
- CU
- Pockets
- 4 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 0% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Nitrite reductase (EC 1.7.99.3) | protein | 330 | 0% helix, 0% strand | P81445 |
Ligands and binding sites
- CU · Copper (II) ion · metal · 6 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1101 | 0.71 | 0.74 | 146 | empty |
| 2 | 1163 | 0.71 | 0.73 | 173 | empty |
| 3 | 875 | 0.70 | 0.74 | 115 | empty |
| 4 | 81 | 0.35 | 0.74 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–C · 412 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 410 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 401 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 1NDR · Crystallographic structure of a blue copper nitrite reductase from alcaligenes… · the same entry in another collection · chain A against A, TM-score 1.00
- P81445 · AlphaFold monomer V2.0 prediction for copper-containing nitrite reductase (P81445) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P81445
- Elsewhere: RCSB PDB 1NDR · PDBe 1NDR · UniProt P81445
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