Research workbench
Crystal structure of the periplasmic nitrate reductase (nap) from escherichia COLI
Analyse Crystal structure of the periplasmic nitrate reductase (nap) from escherichia… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2NYA
- Type
- protein
- Length
- 1,582 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Periplasmic nitrate reductase
- EC
- 1.7.99.4
- UniProt
- P33937
- Ligands
- MGD, SF4, 6MO
- Pockets
- 12 · best druggability 0.88
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | Periplasmic nitrate reductase (EC 1.7.99.4) | protein | 791 | 34% helix, 19% strand | P33937 |
Ligands and binding sites
- MGD · 2-amino-5,6-dimercapto-7-methyl-3,7,8A,9-tetrahydro-8-oxa-1,3,9,10-tetraaza-anthracen-4-one guanosine dinucleotide · ligand · 4 copies · chains A, F
- SF4 · Iron/sulfur cluster · ligand · 2 copies · chains A, F
- 6MO · Molybdenum(vi) ion · metal · 2 copies · chains A, F
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 | 365 | 0.88 | 0.97 | 75 | 6MO, MGD |
| 2 | 837 | 0.84 | 0.87 | 68 | empty |
| 3 | 197 | 0.82 | 0.96 | 44 | 6MO, MGD |
| 4 | 173 | 0.82 | 0.97 | 42 | MGD |
| 5 | 257 | 0.50 | 0.74 | 42 | empty |
Interfaces
1 interface between chains.
- A–F · 939 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 2NYA · Crystal structure of the periplasmic nitrate reductase (NAP) from Escherichia coli · the same entry in another collection · chain A against A, TM-score 1.00
- P33937 · AlphaFold monomer V2.0 prediction for periplasmic nitrate reductase (P33937) · a predicted model of the same protein · 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 P33937
- Elsewhere: RCSB PDB 2NYA · PDBe 2NYA · UniProt P33937
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